Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xcw Working: n-9-19.cluster.ucsf.bkslab.org:/scratch/xiaobo/121205/xcw-8058088.75 Result: /scratch/xiaobo/121205/xcw-8058088.75 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xcw 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/xcw mkdir: created directory `/scratch/xiaobo/121205' mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75' /scratch/xiaobo/121205/xcw-8058088.75 /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/121205/xcw-8058088.75/working' mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/protonate' Storing results in /scratch/xiaobo/121205/xcw-8058088.75/finished Working in /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 /scratch/xiaobo/121205/xcw-8058088.75/working/protonate /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Using inputs as protomers/tautomers. No processing done 457 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/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Bulk generating 3D conformations all protomers in /scratch/xiaobo/121205/xcw-8058088.75/working/3D mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/121205/xcw-8058088.75/working/protonate/xcw-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' 1001 3D conformations generated for 1000 compounds Building ZINC000195127773 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building' mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000195127773 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/1 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCOCC1) `ZINC000195127773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195127773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195127773 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 12, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 24, 38, 38, 38, 38, 38, 24, 24, 24, 14, 14, 2, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195127773 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/finished' Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773/0.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195127773 Building ZINC000195129105 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195129105 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/2 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195129105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129105 none C[C@@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 23, 29, 29, 29, 29, 29, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 10, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/3 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195129105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129105 none C[C@@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 14, 27, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 4, 7, 7, 7, 7, 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]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195129105 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 Building ZINC000195129105 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195129105 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 2) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195129105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129105 none C[C@@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 23, 29, 29, 29, 29, 29, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 10, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 3) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195129105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129105 none C[C@@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 14, 27, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 4, 7, 7, 7, 7, 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]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195129105 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129105 Building ZINC000195129114 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195129114 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/4 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195129114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129114 none C[C@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 14, 26, 31, 31, 31, 31, 31, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 26, 26, 31, 31, 31, 31, 31, 31, 31, 31, 4, 7, 7, 7, 7, 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]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/5 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195129114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129114 none C[C@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 30, 30, 30, 30, 30, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 11, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 3, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195129114 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 Building ZINC000195129114 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195129114 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 4) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195129114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129114 none C[C@H](CN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 14, 26, 31, 31, 31, 31, 31, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 26, 26, 31, 31, 31, 31, 31, 31, 31, 31, 4, 7, 7, 7, 7, 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]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 5) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195129114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195129114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000195129114 none C[C@H](CN1CCOCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 30, 30, 30, 30, 30, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 11, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 3, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195129114 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195129114 Building ZINC000195144227 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195144227 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/6 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195144227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195144227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195144227 none COC(=O)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 30, 44, 13, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 28, 27, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/7 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195144227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195144227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195144227 none COC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 30, 44, 13, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 27, 28, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195144227 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 Building ZINC000195144227 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195144227 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 6) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195144227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195144227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195144227 none COC(=O)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 30, 44, 13, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 28, 27, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 7) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195144227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195144227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195144227 none COC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 30, 44, 13, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 27, 28, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195144227 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144227 Building ZINC000195144932 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195144932 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/8 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)cn1) `ZINC000195144932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195144932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195144932 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 17, 21, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 2, 13, 13, 19, 19, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/9 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)cn1) `ZINC000195144932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195144932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195144932 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 19, 23, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 2, 13, 13, 22, 22, 23, 23, 40, 40, 40, 40, 40, 40, 40, 40, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195144932 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 Building ZINC000195144932 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195144932 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 8) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)cn1) `ZINC000195144932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195144932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195144932 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 17, 21, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 2, 13, 13, 19, 19, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 9) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)cn1) `ZINC000195144932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195144932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195144932 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCN2CCOCC2)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 19, 23, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 2, 13, 13, 22, 22, 23, 23, 40, 40, 40, 40, 40, 40, 40, 40, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195144932 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195144932 Building ZINC000195149626 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195149626 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/10 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)cn1) `ZINC000195149626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195149626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195149626 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 26, 26, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/11 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)cn1) `ZINC000195149626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195149626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195149626 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 29, 29, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 4, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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]) total number of confs: 102 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195149626 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 Building ZINC000195149626 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195149626 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 10) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)cn1) `ZINC000195149626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195149626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195149626 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 26, 26, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 11) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)cn1) `ZINC000195149626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195149626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195149626 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCCC2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 29, 29, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 4, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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]) total number of confs: 102 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195149626 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195149626 Building ZINC000195170242 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195170242 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/12 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/13 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/14 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/14' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/15 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/15' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195170242 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 Building ZINC000195170242 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195170242 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 12) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 13) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 14) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 15) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195170242 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 Building ZINC000195170242 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195170242 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 12) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 13) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 14) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 15) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195170242 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 Building ZINC000195170242 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195170242 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 12) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 13) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 14) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 44, 34, 23, 34, 17, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 46, 46, 46, 44, 44, 44, 44, 34, 34, 34, 23, 21, 20, 20, 14, 14, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 15) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195170242.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195170242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000195170242 none COCCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 33, 22, 33, 16, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 45, 42, 42, 42, 42, 33, 33, 33, 22, 21, 18, 18, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195170242 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195170242 Building ZINC000195173479 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195173479 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/16 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000195173479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195173479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000195173479 none NS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 25, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/17 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000195173479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195173479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000195173479 none NS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 26, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195173479 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 Building ZINC000195173479 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195173479 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 16) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000195173479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195173479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000195173479 none NS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 25, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 17) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000195173479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195173479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000195173479 none NS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 26, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195173479 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195173479 Building ZINC000195186248 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195186248 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/18 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/19 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/20 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/20' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/21 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/21' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195186248 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 Building ZINC000195186248 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195186248 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 18) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 19) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 20) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 21) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195186248 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 Building ZINC000195186248 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195186248 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 18) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 19) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 20) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 21) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195186248 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 Building ZINC000195186248 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195186248 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 18) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 19) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 20) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 21) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CCCN2C)cn1) `ZINC000195186248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195186248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000195186248 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCCN2C)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.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, 5, 7, 5, 5, 5, 10, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 26, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 7, 7, 4, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195186248 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195186248 Building ZINC000195223238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195223238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/22 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)cn1) `ZINC000195223238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195223238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195223238 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 24, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/23 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)cn1) `ZINC000195223238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195223238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195223238 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 12, 12, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195223238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 Building ZINC000195223238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195223238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 22) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)cn1) `ZINC000195223238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195223238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195223238 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 24, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 23) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)cn1) `ZINC000195223238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195223238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000195223238 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCNC(=O)C(C)(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 12, 12, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195223238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195223238 Building ZINC000195256261 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195256261 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/24 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195256261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195256261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195256261 none CCOC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 26, 11, 26, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 11, 11, 5, 5, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/25 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195256261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195256261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195256261 none CCOC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 25, 11, 25, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 11, 11, 5, 5, 5, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195256261 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 Building ZINC000195256261 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195256261 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 24) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195256261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195256261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195256261 none CCOC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 26, 11, 26, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 11, 11, 5, 5, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 25) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195256261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195256261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195256261 none CCOC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 25, 11, 25, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 11, 11, 5, 5, 5, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195256261 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195256261 Building ZINC000195291052 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195291052 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/26 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)cn1) `ZINC000195291052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195291052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195291052 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)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.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 18, 26, 26, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 4, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/27 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)cn1) `ZINC000195291052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195291052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195291052 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)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.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 18, 29, 29, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 4, 29, 29, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 93 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195291052 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 Building ZINC000195291052 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195291052 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 26) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)cn1) `ZINC000195291052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195291052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195291052 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)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.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 18, 26, 26, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 4, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 27) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)cn1) `ZINC000195291052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195291052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000195291052 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(C(N)=O)CCCCC2)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.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 18, 29, 29, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 4, 29, 29, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 93 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000195291052 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000195291052 Building ZINC000237471516 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237471516 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/28 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/28' -> `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@H](C)C(=O)O) `ZINC000237471516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237471516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237471516 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 31, 31, 31, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/29 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/29' -> `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@H](C)C(=O)O) `ZINC000237471516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237471516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237471516 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 29, 29, 29, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237471516 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 Building ZINC000237471516 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237471516 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 28) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O) `ZINC000237471516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237471516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237471516 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 31, 31, 31, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 29) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O) `ZINC000237471516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237471516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237471516 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 29, 29, 29, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237471516 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237471516 Building ZINC000237533864 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237533864 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/30 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/30' -> `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@@H](C)C(=O)O) `ZINC000237533864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237533864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237533864 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 28, 28, 28, 138] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 311 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/31 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/31' -> `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@@H](C)C(=O)O) `ZINC000237533864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237533864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237533864 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 293 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237533864 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 Building ZINC000237533864 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237533864 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 30) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O) `ZINC000237533864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237533864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237533864 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 28, 28, 28, 138] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 311 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 31) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O) `ZINC000237533864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237533864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000237533864 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', '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, 7, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 293 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237533864 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237533864 Building ZINC000237677356 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237677356 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/32 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/32' -> `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)NC1(C(=O)O)CC1) `ZINC000237677356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237677356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000237677356 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1 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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 19, 26, 26, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 78, 19, 19, 19, 19] 93 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/33 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/33' -> `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)NC1(C(=O)O)CC1) `ZINC000237677356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237677356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000237677356 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1 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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 25, 25, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 75, 17, 17, 17, 17] 78 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237677356 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 Building ZINC000237677356 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000237677356 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 32) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1) `ZINC000237677356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000237677356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000237677356 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1 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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 19, 26, 26, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 78, 19, 19, 19, 19] 93 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 33) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1) `ZINC000237677356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000237677356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000237677356 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C(=O)O)CC1 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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 25, 25, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 75, 17, 17, 17, 17] 78 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000237677356 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000237677356 Building ZINC000246936127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/34 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/35 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/36 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/36' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/37 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/37' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 Building ZINC000246936127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 34) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 35) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 36) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 37) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 Building ZINC000246936127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 34) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 35) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 36) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 37) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 Building ZINC000246936127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 34) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 35) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 90, 20, 20, 18, 18, 18, 18, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 36) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 37) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000246936127.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936127 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 21, 32, 32, 18, 18, 18, 18, 13, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 96, 21, 21, 18, 18, 18, 18, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936127 Building ZINC000246936155 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936155 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/38 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/39 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/40 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/40' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/41 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/41' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936155 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 Building ZINC000246936155 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936155 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 38) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 39) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 40) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 41) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936155 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 Building ZINC000246936155 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936155 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 38) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 39) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 40) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 41) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936155 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 Building ZINC000246936155 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000246936155 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 38) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 39) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 31, 31, 16, 16, 16, 16, 15, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 31, 31, 31, 93, 21, 21, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 40) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 41) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C) `ZINC000246936155.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000246936155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000246936155 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 9, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000246936155 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000246936155 Building ZINC000263827792 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263827792 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/42 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)cn1) `ZINC000263827792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263827792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827792 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 6, 13, 23, 23, 13, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 21, 21, 21, 7] 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]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/43 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)cn1) `ZINC000263827792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263827792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827792 none Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 6, 13, 26, 26, 13, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 21, 21, 21, 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]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263827792 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 Building ZINC000263827792 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263827792 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 42) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)cn1) `ZINC000263827792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263827792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827792 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 6, 13, 23, 23, 13, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 21, 21, 21, 7] 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]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 43) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)cn1) `ZINC000263827792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263827792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827792 none Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 6, 13, 26, 26, 13, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 21, 21, 21, 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]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263827792 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827792 Building ZINC000263827793 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263827793 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/44 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)cn1) `ZINC000263827793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263827793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827793 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 13, 28, 28, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 22, 22, 22, 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]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/45 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)cn1) `ZINC000263827793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263827793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827793 none Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 11, 21, 21, 11, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263827793 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 Building ZINC000263827793 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263827793 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 44) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)cn1) `ZINC000263827793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263827793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827793 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 13, 28, 28, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 22, 22, 22, 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]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 45) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)cn1) `ZINC000263827793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263827793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000263827793 none Cn1cc([C@]([O-])([SiH3])C(=O)N(C2CC2)[C@H]2CC(=O)NC2=O)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.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 11, 21, 21, 11, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 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]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263827793 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263827793 Building ZINC000263851277 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263851277 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/46 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263851277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851277 none COC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 20, 36, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 20, 20, 20, 12, 12, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/47 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263851277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851277 none COC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 34, 12, 21, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 21, 21, 21, 12, 12, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263851277 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 Building ZINC000263851277 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263851277 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 46) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263851277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851277 none COC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 20, 36, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 20, 20, 20, 12, 12, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 47) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263851277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851277 none COC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 34, 12, 21, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 21, 21, 21, 12, 12, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263851277 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851277 Building ZINC000263851278 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263851278 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/48 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263851278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851278 none COC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 17, 31, 12, 17, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 17, 17, 17, 12, 12, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/49 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263851278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851278 none COC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 20, 35, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 20, 20, 20, 11, 11, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263851278 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 Building ZINC000263851278 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263851278 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 48) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263851278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851278 none COC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 17, 31, 12, 17, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 17, 17, 17, 12, 12, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 49) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263851278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263851278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000263851278 none COC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 20, 35, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 20, 20, 20, 11, 11, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263851278 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263851278 Building ZINC000263860428 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263860428 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/50 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263860428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860428 none CN(C)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 7, 7, 7, 7, 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]) total number of confs: 90 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/51 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263860428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860428 none CN(C)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263860428 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 Building ZINC000263860428 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263860428 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 50) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263860428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860428 none CN(C)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 7, 7, 7, 7, 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]) total number of confs: 90 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 51) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263860428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860428 none CN(C)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263860428 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860428 Building ZINC000263860429 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263860429 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/52 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263860429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860429 none CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 25, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/53 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263860429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860429 none CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 34, 11, 26, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263860429 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 Building ZINC000263860429 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000263860429 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 52) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000263860429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860429 none CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 25, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 53) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000263860429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000263860429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000263860429 none CN(C)C(=O)[C@@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 34, 11, 26, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000263860429 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000263860429 Building ZINC000264128880 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264128880 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/54 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264128880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264128880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000264128880 none COCCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 2, 5, 10, 10, 17, 17, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 18, 14, 14, 11, 11, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/55 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264128880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264128880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000264128880 none COCCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 11, 5, 2, 5, 9, 9, 16, 16, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 14, 14, 11, 11, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264128880 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 Building ZINC000264128880 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264128880 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 54) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264128880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264128880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000264128880 none COCCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 2, 5, 10, 10, 17, 17, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 18, 14, 14, 11, 11, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 55) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264128880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264128880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000264128880 none COCCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 11, 5, 2, 5, 9, 9, 16, 16, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 14, 14, 11, 11, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264128880 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264128880 Building ZINC000264154022 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264154022 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/56 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264154022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264154022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264154022 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 8, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 26, 26, 26, 26, 26, 15, 15, 15, 15, 8, 8, 8, 8, 8, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/57 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264154022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264154022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264154022 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 8, 8, 8, 8, 8, 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]) total number of confs: 102 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264154022 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 Building ZINC000264154022 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264154022 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 56) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264154022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264154022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264154022 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 8, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 26, 26, 26, 26, 26, 15, 15, 15, 15, 8, 8, 8, 8, 8, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 57) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264154022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264154022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264154022 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 30, 30, 30, 30, 30, 18, 18, 18, 18, 8, 8, 8, 8, 8, 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]) total number of confs: 102 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264154022 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264154022 Building ZINC000264254212 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264254212 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/58 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1) `ZINC000264254212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264254212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264254212 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 7, 16, 16, 16, 16, 33, 50, 50, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 33, 33, 50, 50, 16, 16, 16, 16, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/59 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1) `ZINC000264254212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264254212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264254212 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 37, 50, 50, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 37, 37, 50, 50, 16, 16, 16, 16, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264254212 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 Building ZINC000264254212 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264254212 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 58) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1) `ZINC000264254212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264254212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264254212 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 7, 16, 16, 16, 16, 33, 50, 50, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 33, 33, 50, 50, 16, 16, 16, 16, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 59) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1) `ZINC000264254212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264254212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264254212 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(CC(N)=O)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 37, 50, 50, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 37, 37, 50, 50, 16, 16, 16, 16, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264254212 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264254212 Building ZINC000264368561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264368561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/60 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264368561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264368561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000264368561 none COC(=O)CSCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 28, 44, 15, 8, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 28, 28, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/61 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264368561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264368561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000264368561 none COC(=O)CSCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 29, 44, 16, 8, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 29, 29, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264368561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 Building ZINC000264368561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264368561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 60) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264368561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264368561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000264368561 none COC(=O)CSCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 28, 44, 15, 8, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 28, 28, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 61) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000264368561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264368561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000264368561 none COC(=O)CSCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 29, 44, 16, 8, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 44, 44, 44, 29, 29, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264368561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264368561 Building ZINC000264421137 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264421137 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/62 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264421137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421137 none CC[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 22, 30, 30, 11, 11, 11, 11, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 32, 32, 32, 32, 32, 90, 22, 22, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/63 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264421137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421137 none CC[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 22, 29, 29, 10, 10, 10, 10, 5, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 29, 29, 29, 29, 29, 87, 22, 22, 10, 10, 10, 10, 3, 3, 3, 3, 3, 10, 10, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264421137 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 Building ZINC000264421137 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264421137 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 62) grep: /scratch/xiaobo/121205/xcw-8058088.75/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@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264421137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421137 none CC[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 22, 30, 30, 11, 11, 11, 11, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 32, 32, 32, 32, 32, 90, 22, 22, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 63) grep: /scratch/xiaobo/121205/xcw-8058088.75/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@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264421137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421137 none CC[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 22, 29, 29, 10, 10, 10, 10, 5, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 29, 29, 29, 29, 29, 87, 22, 22, 10, 10, 10, 10, 3, 3, 3, 3, 3, 10, 10, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264421137 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421137 Building ZINC000264421139 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264421139 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/64 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264421139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421139 none CC[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 22, 30, 30, 11, 11, 11, 11, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 32, 32, 32, 32, 32, 90, 22, 22, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/65 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264421139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421139 none CC[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 21, 27, 27, 12, 12, 12, 12, 5, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 28, 28, 28, 28, 28, 81, 21, 21, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12, 12, 12] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264421139 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 Building ZINC000264421139 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264421139 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 64) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264421139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421139 none CC[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 22, 30, 30, 11, 11, 11, 11, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 32, 32, 32, 32, 32, 90, 22, 22, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 65) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264421139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264421139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000264421139 none CC[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 21, 27, 27, 12, 12, 12, 12, 5, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 28, 28, 28, 28, 28, 81, 21, 21, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12, 12, 12] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264421139 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264421139 Building ZINC000264568999 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264568999 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/66 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264568999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264568999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264568999 none CCNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 16, 22, 16, 16, 16, 6, 1, 11, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 34, 34, 34, 34, 34, 22, 16, 16, 16, 16, 4, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/67 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264568999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264568999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264568999 none CCNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 16, 23, 16, 16, 16, 6, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 33, 33, 33, 33, 33, 23, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264568999 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 Building ZINC000264568999 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264568999 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 66) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264568999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264568999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264568999 none CCNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 16, 22, 16, 16, 16, 6, 1, 11, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 34, 34, 34, 34, 34, 22, 16, 16, 16, 16, 4, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 67) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264568999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264568999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000264568999 none CCNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 16, 23, 16, 16, 16, 6, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 33, 33, 33, 33, 33, 23, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264568999 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264568999 Building ZINC000264588979 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588979 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/68 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/69 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/70 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/70' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/71 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/71' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588979 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 Building ZINC000264588979 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588979 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 68) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 69) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 70) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 71) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588979 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 Building ZINC000264588979 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588979 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 68) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 69) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 70) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 71) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588979 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 Building ZINC000264588979 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588979 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 68) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 69) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 70) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 37, 37, 37, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 71) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588979 none COCCN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 17, 17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 39, 39, 39, 34, 34, 34, 34, 17, 17, 17, 17, 2, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588979 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588979 Building ZINC000264588980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/72 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/73 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/74 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/74' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/75 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/75' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 Building ZINC000264588980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 72) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 73) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 74) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 75) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 Building ZINC000264588980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 72) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 73) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 74) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 75) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 Building ZINC000264588980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000264588980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 72) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 73) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 74) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens 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, 35, 35, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 35, 35, 35, 35, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 75) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000264588980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000264588980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000264588980 none COCCN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', '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'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 19, 37, 37, 37, 34, 34, 34, 34, 19, 19, 19, 19, 2, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264588980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264588980 Building ZINC000264725831 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264725831 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/76 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000264725831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000264725831 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 39 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]) total number of confs: 34 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/77 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000264725831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000264725831 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 40 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264725831 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 Building ZINC000264725831 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264725831 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 76) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000264725831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000264725831 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 39 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]) total number of confs: 34 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 77) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000264725831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000264725831 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 40 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264725831 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264725831 Building ZINC000264822866 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264822866 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/78 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCSCC2)cn1) `ZINC000264822866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264822866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000264822866 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCSCC2)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.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 27, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 2, 13, 13, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/79 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCSCC2)cn1) `ZINC000264822866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264822866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000264822866 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCSCC2)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.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 14, 27, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 2, 14, 14, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 7] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264822866 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 Building ZINC000264822866 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264822866 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 78) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCSCC2)cn1) `ZINC000264822866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264822866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000264822866 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCSCC2)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.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 27, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 2, 13, 13, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 79) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCSCC2)cn1) `ZINC000264822866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264822866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000264822866 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCSCC2)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.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 14, 27, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 2, 14, 14, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 7] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264822866 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264822866 Building ZINC000264888498 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264888498 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/80 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264888498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264888498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000264888498 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 19, 9, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 32, 32, 32, 27, 27, 19, 19, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/81 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264888498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264888498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000264888498 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 29, 22, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 35, 35, 35, 29, 29, 22, 22, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264888498 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 Building ZINC000264888498 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264888498 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 80) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264888498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264888498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000264888498 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 19, 9, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 32, 32, 32, 27, 27, 19, 19, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 81) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000264888498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264888498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000264888498 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 29, 22, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 35, 35, 35, 29, 29, 22, 22, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264888498 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264888498 Building ZINC000264966670 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264966670 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/82 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1) `ZINC000264966670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264966670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264966670 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 30, 30, 49, 49, 49, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/83 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1) `ZINC000264966670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264966670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264966670 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 30, 30, 49, 49, 49, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264966670 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 Building ZINC000264966670 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000264966670 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 82) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1) `ZINC000264966670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000264966670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264966670 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 30, 30, 49, 49, 49, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 83) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1) `ZINC000264966670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000264966670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000264966670 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 30, 30, 49, 49, 49, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000264966670 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000264966670 Building ZINC000265068533 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265068533 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/84 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1) `ZINC000265068533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265068533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000265068533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 30, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 30, 30, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/85 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1) `ZINC000265068533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265068533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000265068533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 7, 12, 12, 12, 12, 28, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265068533 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 Building ZINC000265068533 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265068533 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 84) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1) `ZINC000265068533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265068533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000265068533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 30, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 30, 30, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 85) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1) `ZINC000265068533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265068533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000265068533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 7, 12, 12, 12, 12, 28, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265068533 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265068533 Building ZINC000265126355 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265126355 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/86 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265126355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126355 none COC(=O)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 18, 34, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 18, 18, 8, 8, 8, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/87 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265126355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126355 none COC(=O)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 25, 37, 9, 4, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265126355 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 Building ZINC000265126355 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265126355 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 86) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265126355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126355 none COC(=O)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 18, 34, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 18, 18, 8, 8, 8, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 87) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265126355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126355 none COC(=O)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 25, 37, 9, 4, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265126355 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126355 Building ZINC000265126357 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265126357 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/88 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265126357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126357 none COC(=O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 36, 9, 4, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/89 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265126357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126357 none COC(=O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 35, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 18, 18, 8, 8, 8, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265126357 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 Building ZINC000265126357 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265126357 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 88) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265126357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126357 none COC(=O)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 36, 9, 4, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 89) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000265126357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265126357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000265126357 none COC(=O)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 35, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 18, 18, 8, 8, 8, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265126357 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265126357 Building ZINC000265235714 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265235714 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/90 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)cn1) `ZINC000265235714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265235714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265235714 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)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.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 27, 31, 31, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 3, 11, 11, 31, 31, 27, 27, 27, 27, 27, 27, 27, 27, 7] 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/91 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)cn1) `ZINC000265235714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265235714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265235714 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)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.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 29, 34, 34, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 4, 14, 14, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265235714 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 Building ZINC000265235714 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265235714 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 90) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)cn1) `ZINC000265235714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265235714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265235714 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)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.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 27, 31, 31, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 3, 11, 11, 31, 31, 27, 27, 27, 27, 27, 27, 27, 27, 7] 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 91) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)cn1) `ZINC000265235714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265235714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265235714 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(N)=O)CCCC2)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.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 29, 34, 34, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 4, 14, 14, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265235714 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265235714 Building ZINC000265516513 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265516513 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/92 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O) `ZINC000265516513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265516513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265516513 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 30, 30, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/93 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O) `ZINC000265516513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265516513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265516513 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 17, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 30, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265516513 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 Building ZINC000265516513 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265516513 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 92) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O) `ZINC000265516513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265516513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265516513 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 30, 30, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 93) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O) `ZINC000265516513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265516513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000265516513 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 17, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 30, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265516513 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516513 Building ZINC000265516559 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265516559 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/94 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O) `ZINC000265516559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265516559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000265516559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 16, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 26, 26, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/95 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O) `ZINC000265516559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265516559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000265516559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 26, 26, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265516559 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 Building ZINC000265516559 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265516559 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 94) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O) `ZINC000265516559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265516559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000265516559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 16, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 26, 26, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 95) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O) `ZINC000265516559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265516559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000265516559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 26, 26, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265516559 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265516559 Building ZINC000265667459 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265667459 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/96 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265667459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667459 none CC(C)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 27, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 20, 20, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/97 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265667459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667459 none CC(C)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 23, 34, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 4, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265667459 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 Building ZINC000265667459 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265667459 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 96) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265667459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667459 none CC(C)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 27, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 20, 20, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 97) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265667459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667459 none CC(C)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 23, 34, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 4, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265667459 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667459 Building ZINC000265667460 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265667460 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/98 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265667460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667460 none CC(C)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 23, 34, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 4, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/99 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265667460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667460 none CC(C)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 20, 20, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265667460 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 Building ZINC000265667460 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265667460 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 98) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265667460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667460 none CC(C)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 23, 34, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 4, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 99) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000265667460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265667460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265667460 none CC(C)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 20, 20, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265667460 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265667460 Building ZINC000265864378 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265864378 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/100 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/100' -> `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)N1CCN(C)C(=O)C1) `ZINC000265864378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265864378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265864378 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 13, 22, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31] 39 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/101 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/101' -> `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)N1CCN(C)C(=O)C1) `ZINC000265864378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265864378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265864378 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 23, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 34, 34] 46 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265864378 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 Building ZINC000265864378 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000265864378 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 100) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1) `ZINC000265864378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000265864378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265864378 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 13, 22, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31] 39 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 101) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1) `ZINC000265864378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000265864378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000265864378 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 11, 23, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 34, 34] 46 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000265864378 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000265864378 Building ZINC000266089668 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266089668 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/102 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O) `ZINC000266089668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266089668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266089668 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 28, 46, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 28, 28, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/103 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O) `ZINC000266089668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266089668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266089668 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 30, 47, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 30, 30, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266089668 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 Building ZINC000266089668 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266089668 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 102) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O) `ZINC000266089668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266089668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266089668 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 28, 46, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 28, 28, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 103) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O) `ZINC000266089668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266089668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266089668 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 30, 47, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 30, 30, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266089668 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266089668 Building ZINC000266388659 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388659 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/104 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)cn1) `ZINC000266388659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388659 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 19, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 3, 16, 16, 31, 31, 31, 31, 31, 31, 93, 8] 150 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/105 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)cn1) `ZINC000266388659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388659 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 3, 16, 16, 30, 30, 30, 30, 30, 30, 90, 8] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388659 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 Building ZINC000266388659 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388659 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 104) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)cn1) `ZINC000266388659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388659 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 19, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 3, 16, 16, 31, 31, 31, 31, 31, 31, 93, 8] 150 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 105) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)cn1) `ZINC000266388659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388659 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 3, 16, 16, 30, 30, 30, 30, 30, 30, 90, 8] 150 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388659 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388659 Building ZINC000266388661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/106 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)cn1) `ZINC000266388661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388661 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 2, 12, 12, 34, 34, 34, 34, 34, 34, 102, 6] 150 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/107 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)cn1) `ZINC000266388661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388661 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 12, 12, 31, 31, 31, 31, 31, 31, 93, 6] 150 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 Building ZINC000266388661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 106) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)cn1) `ZINC000266388661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388661 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 2, 12, 12, 34, 34, 34, 34, 34, 34, 102, 6] 150 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 107) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)cn1) `ZINC000266388661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388661 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 12, 12, 31, 31, 31, 31, 31, 31, 93, 6] 150 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388661 Building ZINC000266388663 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388663 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/108 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)cn1) `ZINC000266388663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388663 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 2, 10, 10, 27, 27, 27, 27, 27, 27, 81, 5] 150 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/109 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)cn1) `ZINC000266388663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388663 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 12, 12, 30, 30, 30, 30, 30, 30, 90, 6] 150 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388663 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 Building ZINC000266388663 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388663 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 108) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)cn1) `ZINC000266388663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388663 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 2, 10, 10, 27, 27, 27, 27, 27, 27, 81, 5] 150 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 109) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)cn1) `ZINC000266388663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388663 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 12, 12, 30, 30, 30, 30, 30, 30, 90, 6] 150 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388663 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388663 Building ZINC000266388666 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388666 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/110 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)cn1) `ZINC000266388666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388666 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 3, 16, 16, 30, 30, 30, 30, 30, 30, 90, 7] 150 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/111 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)cn1) `ZINC000266388666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388666 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 21, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 3, 16, 16, 32, 32, 32, 32, 32, 32, 96, 8] 150 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388666 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 Building ZINC000266388666 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266388666 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 110) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)cn1) `ZINC000266388666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266388666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388666 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 3, 16, 16, 30, 30, 30, 30, 30, 30, 90, 7] 150 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 111) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)cn1) `ZINC000266388666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266388666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000266388666 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H]2O)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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 21, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 3, 16, 16, 32, 32, 32, 32, 32, 32, 96, 8] 150 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266388666 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266388666 Building ZINC000266791855 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266791855 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/112 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O) `ZINC000266791855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266791855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791855 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 9, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16] 19 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/113 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O) `ZINC000266791855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266791855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791855 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 14 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266791855 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 Building ZINC000266791855 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266791855 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 112) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O) `ZINC000266791855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266791855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791855 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 9, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16] 19 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 113) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O) `ZINC000266791855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266791855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791855 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 14 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266791855 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791855 Building ZINC000266791857 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266791857 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/114 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O) `ZINC000266791857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266791857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791857 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/115 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O) `ZINC000266791857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266791857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791857 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 8, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14] 17 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266791857 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 Building ZINC000266791857 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266791857 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 114) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O) `ZINC000266791857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266791857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791857 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 115) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O) `ZINC000266791857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266791857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000266791857 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 8, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14] 17 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266791857 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266791857 Building ZINC000266926814 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266926814 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/116 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000266926814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266926814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000266926814 none CCOC(=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 17, 49, 13, 17, 13, 13, 13, 8, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/117 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000266926814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266926814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000266926814 none CCOC(=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 19, 48, 12, 19, 12, 12, 12, 8, 2, 11, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266926814 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 Building ZINC000266926814 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000266926814 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 116) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000266926814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000266926814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000266926814 none CCOC(=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 17, 49, 13, 17, 13, 13, 13, 8, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 117) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000266926814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000266926814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000266926814 none CCOC(=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 19, 48, 12, 19, 12, 12, 12, 8, 2, 11, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000266926814 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000266926814 Building ZINC000267306654 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306654 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/118 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306654 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 9] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/119 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306654 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 9, 9, 9, 9, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 9] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306654 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 Building ZINC000267306654 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306654 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 118) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306654 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 9] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 119) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306654 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 9, 9, 9, 9, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 9] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306654 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306654 Building ZINC000267306656 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306656 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/120 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306656 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 32, 32, 9, 9, 9, 9, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 32, 32, 9] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/121 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306656 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 9] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306656 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 Building ZINC000267306656 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306656 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 120) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306656 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 32, 32, 9, 9, 9, 9, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 32, 32, 9] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 121) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306656 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 9] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306656 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306656 Building ZINC000267306657 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306657 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/122 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306657 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 11] 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]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/123 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306657 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12, 12, 12, 12, 12, 12, 5, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12] 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306657 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 Building ZINC000267306657 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306657 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 122) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306657 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 11] 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]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 123) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)cn1) `ZINC000267306657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306657 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12, 12, 12, 12, 12, 12, 5, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12] 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306657 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306657 Building ZINC000267306659 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306659 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/124 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306659 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12, 12, 12, 12, 12, 12, 5, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12] 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]) total number of confs: 103 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/125 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306659 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 11] 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]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306659 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 Building ZINC000267306659 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267306659 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 124) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267306659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306659 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12, 12, 12, 12, 12, 12, 5, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 12] 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]) total number of confs: 103 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 125) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)cn1) `ZINC000267306659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267306659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000267306659 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2C(N)=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 11] 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]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267306659 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267306659 Building ZINC000267604141 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267604141 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/126 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267604141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604141 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 20, 20, 20, 20, 5, 20, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 31, 31, 31, 31, 31, 31, 31, 20, 20, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/127 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267604141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604141 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 30, 30, 30, 30, 30, 30, 30, 20, 20, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267604141 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 Building ZINC000267604141 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267604141 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 126) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267604141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604141 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 20, 20, 20, 20, 5, 20, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 31, 31, 31, 31, 31, 31, 31, 20, 20, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 127) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267604141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604141 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 30, 30, 30, 30, 30, 30, 30, 20, 20, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267604141 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604141 Building ZINC000267604143 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267604143 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/128 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267604143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604143 none CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 36, 29, 29, 29, 29, 8, 29, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 36, 36, 36, 36, 36, 36, 36, 29, 29, 5, 10, 10, 10, 10, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/129 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267604143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604143 none CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 35, 25, 25, 25, 25, 9, 25, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 35, 35, 35, 35, 35, 35, 35, 25, 25, 5, 11, 11, 11, 11, 11] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267604143 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 Building ZINC000267604143 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267604143 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 128) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267604143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604143 none CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 36, 29, 29, 29, 29, 8, 29, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 36, 36, 36, 36, 36, 36, 36, 29, 29, 5, 10, 10, 10, 10, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 129) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O) `ZINC000267604143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267604143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267604143 none CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 35, 25, 25, 25, 25, 9, 25, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 35, 35, 35, 35, 35, 35, 35, 25, 25, 5, 11, 11, 11, 11, 11] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267604143 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267604143 Building ZINC000267682403 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267682403 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/130 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267682403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267682403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267682403 none COC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 14, 30, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 15, 15, 30, 30, 30, 14, 14, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/131 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267682403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267682403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267682403 none COC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 13, 29, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 15, 15, 29, 29, 29, 13, 13, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267682403 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 Building ZINC000267682403 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267682403 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 130) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267682403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267682403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267682403 none COC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 14, 30, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 15, 15, 30, 30, 30, 14, 14, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 131) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267682403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267682403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267682403 none COC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 13, 29, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 15, 15, 29, 29, 29, 13, 13, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267682403 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267682403 Building ZINC000267739129 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267739129 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/132 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267739129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739129 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 20, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 13, 13, 20, 20, 20, 4, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/133 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267739129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739129 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 19, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 10, 18, 18, 19, 19, 19, 4, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267739129 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 Building ZINC000267739129 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267739129 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 132) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267739129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739129 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 20, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 13, 13, 20, 20, 20, 4, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 133) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267739129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739129 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 19, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 10, 18, 18, 19, 19, 19, 4, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267739129 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739129 Building ZINC000267739133 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267739133 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/134 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267739133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739133 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 24, 4, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 11, 17, 17, 24, 24, 24, 4, 8, 8, 8, 8, 8, 17, 17, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/135 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267739133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739133 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 20, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 13, 13, 20, 20, 20, 4, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267739133 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 Building ZINC000267739133 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267739133 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 134) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267739133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739133 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 24, 4, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 11, 17, 17, 24, 24, 24, 4, 8, 8, 8, 8, 8, 17, 17, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 135) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000267739133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267739133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000267739133 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 20, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 13, 13, 20, 20, 20, 4, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267739133 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267739133 Building ZINC000267822229 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267822229 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/136 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1) `ZINC000267822229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267822229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822229 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/137 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1) `ZINC000267822229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267822229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822229 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 8, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16] 17 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267822229 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 Building ZINC000267822229 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267822229 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 136) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1) `ZINC000267822229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267822229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822229 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 137) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1) `ZINC000267822229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267822229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822229 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 8, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16] 17 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267822229 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822229 Building ZINC000267822231 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267822231 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/138 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1) `ZINC000267822231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267822231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822231 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 2, 7, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16] 17 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/139 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1) `ZINC000267822231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267822231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822231 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 6, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267822231 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 Building ZINC000267822231 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267822231 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 138) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1) `ZINC000267822231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267822231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822231 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 2, 7, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16] 17 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 139) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1) `ZINC000267822231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267822231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000267822231 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)NC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 6, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267822231 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267822231 Building ZINC000267826035 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267826035 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/140 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267826035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826035 none COC(=O)[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 35, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 12, 35, 35, 35, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/141 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267826035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826035 none COC(=O)[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 11, 39, 11, 11, 11, 11, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 11, 39, 39, 39, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267826035 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 Building ZINC000267826035 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267826035 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 140) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267826035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826035 none COC(=O)[C@@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 35, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 12, 35, 35, 35, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 141) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267826035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826035 none COC(=O)[C@@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 11, 39, 11, 11, 11, 11, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 11, 39, 39, 39, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267826035 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826035 Building ZINC000267826036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267826036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/142 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267826036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826036 none COC(=O)[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 11, 33, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 11, 33, 33, 33, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/143 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267826036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826036 none COC(=O)[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 10, 39, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 10, 39, 39, 39, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267826036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 Building ZINC000267826036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000267826036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 142) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000267826036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826036 none COC(=O)[C@]1(F)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 11, 33, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 11, 33, 33, 33, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 143) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000267826036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000267826036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000267826036 none COC(=O)[C@]1(F)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 10, 39, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 10, 39, 39, 39, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000267826036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000267826036 Building ZINC000268355713 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355713 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/144 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1) `ZINC000268355713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355713 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/145 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1) `ZINC000268355713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355713 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 32, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355713 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 Building ZINC000268355713 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355713 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 144) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1) `ZINC000268355713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355713 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 145) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1) `ZINC000268355713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355713 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 32, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355713 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355713 Building ZINC000268355717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/146 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1) `ZINC000268355717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 20, 38, 38, 38, 38, 38, 38, 50, 50, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 13, 13, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/147 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1) `ZINC000268355717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 43, 43, 43, 43, 43, 43, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 43, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 Building ZINC000268355717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 146) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1) `ZINC000268355717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 20, 38, 38, 38, 38, 38, 38, 50, 50, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 13, 13, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 147) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1) `ZINC000268355717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 43, 43, 43, 43, 43, 43, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 43, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355717 Building ZINC000268355720 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355720 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/148 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355720 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 43, 43, 43, 43, 43, 43, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 43, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/149 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355720 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 21, 40, 40, 40, 40, 40, 40, 50, 50, 40, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 40, 40, 40, 40, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355720 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 Building ZINC000268355720 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355720 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 148) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355720 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 43, 43, 43, 43, 43, 43, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 43, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 149) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355720 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 21, 40, 40, 40, 40, 40, 40, 50, 50, 40, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 40, 40, 40, 40, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355720 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355720 Building ZINC000268355721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/150 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/151 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 47, 47, 47, 47, 47, 47, 50, 50, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 Building ZINC000268355721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268355721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 150) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268355721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 48, 48, 48, 48, 48, 48, 50, 50, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 48, 48, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 151) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1) `ZINC000268355721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268355721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000268355721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 47, 47, 47, 47, 47, 47, 50, 50, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268355721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268355721 Building ZINC000268476044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268476044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/152 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268476044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268476044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000268476044 none COC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 4, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/153 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268476044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268476044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000268476044 none COC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 6, 16, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 16, 16, 16, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268476044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 Building ZINC000268476044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268476044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 152) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268476044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268476044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000268476044 none COC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 4, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 153) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268476044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268476044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000268476044 none COC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 6, 16, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 16, 16, 16, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268476044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268476044 Building ZINC000268943040 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268943040 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/154 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC(=O)O)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268943040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268943040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000268943040 none COCCN(CC(=O)O)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 11, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 15, 5, 2, 5, 12, 16, 16, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 23, 23, 15, 15, 12, 12, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 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]) total number of confs: 209 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/155 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC(=O)O)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268943040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268943040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000268943040 none COCCN(CC(=O)O)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 11, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 23, 15, 5, 2, 5, 8, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 23, 23, 15, 15, 8, 8, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 210 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268943040 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 Building ZINC000268943040 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268943040 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 154) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(CC(=O)O)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268943040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268943040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000268943040 none COCCN(CC(=O)O)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 11, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 15, 5, 2, 5, 12, 16, 16, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 23, 23, 15, 15, 12, 12, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 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]) total number of confs: 209 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 155) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN(CC(=O)O)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000268943040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268943040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000268943040 none COCCN(CC(=O)O)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 11, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 23, 15, 5, 2, 5, 8, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 23, 23, 15, 15, 8, 8, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 210 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268943040 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268943040 Building ZINC000268995091 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268995091 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/156 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/156' -> `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)N1CCOC[C@@H]1C(=O)O) `ZINC000268995091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268995091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995091 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 51] 66 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/157 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/157' -> `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)N1CCOC[C@@H]1C(=O)O) `ZINC000268995091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268995091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995091 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 57] 75 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268995091 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 Building ZINC000268995091 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268995091 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 156) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O) `ZINC000268995091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268995091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995091 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 51] 66 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 157) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O) `ZINC000268995091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268995091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995091 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 57] 75 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268995091 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995091 Building ZINC000268995092 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268995092 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/158 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/158' -> `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)N1CCOC[C@H]1C(=O)O) `ZINC000268995092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268995092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995092 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 57] 72 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/159 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/159' -> `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)N1CCOC[C@H]1C(=O)O) `ZINC000268995092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268995092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995092 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 48] 63 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268995092 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 Building ZINC000268995092 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268995092 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 158) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O) `ZINC000268995092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268995092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995092 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 57] 72 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 159) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O) `ZINC000268995092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268995092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000268995092 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 48] 63 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000268995092 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000268995092 Building ZINC000269089521 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269089521 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/160 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO) `ZINC000269089521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269089521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000269089521 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 40, 46, 13, 13, 3, 3, 3, 3, 3, 19, 40, 40, 46, 46, 138] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/161 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO) `ZINC000269089521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269089521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000269089521 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 40, 46, 13, 13, 3, 3, 3, 3, 3, 20, 40, 40, 46, 46, 138] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269089521 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 Building ZINC000269089521 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269089521 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 160) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO) `ZINC000269089521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269089521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000269089521 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 40, 46, 13, 13, 3, 3, 3, 3, 3, 19, 40, 40, 46, 46, 138] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 161) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO) `ZINC000269089521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269089521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000269089521 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NCCO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 40, 46, 13, 13, 3, 3, 3, 3, 3, 20, 40, 40, 46, 46, 138] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269089521 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269089521 Building ZINC000269098863 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269098863 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/162 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1) `ZINC000269098863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269098863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000269098863 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 21, 21, 21, 41, 47, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 21, 41, 41, 47, 47, 141, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/163 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1) `ZINC000269098863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269098863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000269098863 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 20, 20, 20, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 20, 42, 42, 47, 47, 141, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269098863 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 Building ZINC000269098863 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269098863 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 162) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1) `ZINC000269098863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269098863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000269098863 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 21, 21, 21, 41, 47, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 21, 41, 41, 47, 47, 141, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 163) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1) `ZINC000269098863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269098863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000269098863 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCC(=O)NCCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 20, 20, 20, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 20, 42, 42, 47, 47, 141, 3, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269098863 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269098863 Building ZINC000269362581 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269362581 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/164 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000269362581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269362581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000269362581 none COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 18, 18, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 18, 33, 33, 33, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/165 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000269362581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269362581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000269362581 none COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 36, 19, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 19, 36, 36, 36, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269362581 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 Building ZINC000269362581 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269362581 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 164) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000269362581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269362581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000269362581 none COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 18, 18, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 18, 33, 33, 33, 18, 18, 18, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 165) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000269362581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269362581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000269362581 none COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 36, 19, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 19, 36, 36, 36, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269362581 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269362581 Building ZINC000269380756 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269380756 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/166 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000269380756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269380756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000269380756 none COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 13, 13, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 13, 25, 25, 25, 13, 13, 13, 5, 11, 11, 11, 11, 11, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/167 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000269380756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269380756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000269380756 none COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 17, 26, 26, 26, 17, 17, 17, 5, 12, 12, 12, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269380756 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 Building ZINC000269380756 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269380756 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 166) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000269380756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269380756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000269380756 none COC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 13, 13, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 13, 25, 25, 25, 13, 13, 13, 5, 11, 11, 11, 11, 11, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 167) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000269380756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269380756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000269380756 none COC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 5, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 17, 26, 26, 26, 17, 17, 17, 5, 12, 12, 12, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269380756 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269380756 Building ZINC000269592841 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269592841 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/168 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/168' -> `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)NC[C@@H](C)CO) `ZINC000269592841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269592841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592841 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 39, 39, 37, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 39, 39, 39, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/169 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/169' -> `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)NC[C@@H](C)CO) `ZINC000269592841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269592841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592841 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 45, 42, 45, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 45, 45, 45, 50, 50, 150] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269592841 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 Building ZINC000269592841 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269592841 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 168) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)CO) `ZINC000269592841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269592841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592841 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 39, 39, 37, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 39, 39, 39, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 169) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)CO) `ZINC000269592841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269592841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592841 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 45, 42, 45, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 45, 45, 45, 50, 50, 150] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269592841 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592841 Building ZINC000269592843 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269592843 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/170 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/170' -> `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)NC[C@H](C)CO) `ZINC000269592843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269592843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592843 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 46, 44, 45, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 46, 46, 46, 50, 50, 150] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 374 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/171 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/171' -> `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)NC[C@H](C)CO) `ZINC000269592843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269592843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592843 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 37, 36, 36, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 37, 37, 37, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 362 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269592843 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 Building ZINC000269592843 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269592843 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 170) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)CO) `ZINC000269592843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269592843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592843 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 46, 44, 45, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 46, 46, 46, 50, 50, 150] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 374 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 171) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)CO) `ZINC000269592843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269592843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000269592843 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)CO 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', '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, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 37, 36, 36, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 37, 37, 37, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 362 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269592843 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269592843 Building ZINC000269948621 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269948621 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/172 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/172' -> `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)NC[C@](C)(O)CN(C)C) `ZINC000269948621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269948621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948621 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 27, 41, 43, 41, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 27, 27, 43, 43, 43, 129, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/173 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/173' -> `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)NC[C@](C)(O)CN(C)C) `ZINC000269948621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269948621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948621 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 21, 40, 40, 38, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 40, 40, 40, 120, 42, 42, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 312 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269948621 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 Building ZINC000269948621 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269948621 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 172) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C) `ZINC000269948621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269948621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948621 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 27, 41, 43, 41, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 27, 27, 43, 43, 43, 129, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 173) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C) `ZINC000269948621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269948621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948621 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 21, 40, 40, 38, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 40, 40, 40, 120, 42, 42, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 312 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269948621 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948621 Building ZINC000269948622 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269948622 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/174 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/174' -> `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)NC[C@@](C)(O)CN(C)C) `ZINC000269948622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269948622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948622 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 43, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 45, 45, 45, 135, 45, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 330 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/175 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/175' -> `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)NC[C@@](C)(O)CN(C)C) `ZINC000269948622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269948622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948622 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 42, 44, 42, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 44, 44, 44, 132, 44, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269948622 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 Building ZINC000269948622 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000269948622 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 174) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C) `ZINC000269948622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000269948622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948622 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 43, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 45, 45, 45, 135, 45, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 330 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 175) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C) `ZINC000269948622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000269948622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000269948622 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 10, 5, 5, 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, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 42, 44, 42, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 44, 44, 44, 132, 44, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000269948622 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000269948622 Building ZINC000270221095 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270221095 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/176 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1) `ZINC000270221095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270221095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221095 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/177 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1) `ZINC000270221095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270221095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221095 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270221095 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 Building ZINC000270221095 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270221095 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 176) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1) `ZINC000270221095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270221095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221095 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 177) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1) `ZINC000270221095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270221095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221095 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270221095 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221095 Building ZINC000270221097 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270221097 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/178 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1) `ZINC000270221097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270221097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221097 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/179 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1) `ZINC000270221097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270221097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221097 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270221097 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 Building ZINC000270221097 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270221097 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 178) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1) `ZINC000270221097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270221097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221097 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4, 4, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 4] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 179) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1) `ZINC000270221097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270221097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270221097 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8, 8, 23, 23, 23, 23, 23, 8, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 8] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270221097 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270221097 Building ZINC000270253212 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253212 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/180 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O) `ZINC000270253212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253212 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 16, 5, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 5, 16, 16, 16, 16, 16, 5, 13, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/181 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O) `ZINC000270253212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253212 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 18, 4, 5, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 4, 18, 18, 18, 18, 18, 4, 11, 11, 11] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253212 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 Building ZINC000270253212 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253212 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 180) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O) `ZINC000270253212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253212 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 16, 5, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 5, 16, 16, 16, 16, 16, 5, 13, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 181) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O) `ZINC000270253212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253212 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 18, 4, 5, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 4, 18, 18, 18, 18, 18, 4, 11, 11, 11] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253212 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253212 Building ZINC000270253215 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253215 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/182 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O) `ZINC000270253215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253215 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 18, 4, 5, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 4, 18, 18, 18, 18, 18, 4, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/183 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O) `ZINC000270253215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253215 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 16, 5, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 5, 16, 16, 16, 16, 16, 5, 13, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253215 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 Building ZINC000270253215 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253215 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 182) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O) `ZINC000270253215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253215 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 18, 4, 5, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 4, 18, 18, 18, 18, 18, 4, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 183) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O) `ZINC000270253215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270253215 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 16, 5, 7, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 5, 16, 16, 16, 16, 16, 5, 13, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253215 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253215 Building ZINC000270253327 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253327 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/184 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1) `ZINC000270253327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253327 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/185 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1) `ZINC000270253327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253327 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 3, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253327 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 Building ZINC000270253327 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253327 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 184) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1) `ZINC000270253327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253327 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 185) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1) `ZINC000270253327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253327 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 3, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253327 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253327 Building ZINC000270253329 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253329 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/186 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1) `ZINC000270253329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253329 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 7, 7, 19, 19, 19, 19, 19, 7, 3, 13, 13, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/187 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1) `ZINC000270253329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253329 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253329 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 Building ZINC000270253329 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270253329 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 186) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1) `ZINC000270253329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270253329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253329 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 7, 7, 19, 19, 19, 19, 19, 7, 3, 13, 13, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 187) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1) `ZINC000270253329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270253329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270253329 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270253329 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270253329 Building ZINC000270265907 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270265907 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/188 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270265907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265907 none CCNC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 3, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 9, 6, 6, 6, 3, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/189 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270265907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265907 none CCNC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 8, 4, 8, 2, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 19, 19, 19, 19, 19, 8, 4, 4, 4, 2, 6, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270265907 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 Building ZINC000270265907 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270265907 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 188) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270265907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265907 none CCNC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 3, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 9, 6, 6, 6, 3, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 189) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270265907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265907 none CCNC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 8, 4, 8, 2, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 19, 19, 19, 19, 19, 8, 4, 4, 4, 2, 6, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270265907 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265907 Building ZINC000270265910 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270265910 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/190 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270265910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265910 none CCNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 5, 9, 2, 5, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 20, 20, 20, 20, 20, 9, 5, 5, 5, 2, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/191 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270265910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265910 none CCNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 3, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 9, 6, 6, 6, 3, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270265910 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 Building ZINC000270265910 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270265910 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 190) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270265910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265910 none CCNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 5, 9, 2, 5, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 20, 20, 20, 20, 20, 9, 5, 5, 5, 2, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 191) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000270265910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270265910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000270265910 none CCNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 3, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 6, 17, 17, 17, 17, 17, 9, 6, 6, 6, 3, 6, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270265910 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270265910 Building ZINC000270268625 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270268625 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/192 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1) `ZINC000270268625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270268625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270268625 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 7, 7, 22, 22, 22, 22, 22, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/193 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1) `ZINC000270268625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270268625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270268625 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 6, 6, 26, 26, 26, 26, 26, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270268625 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 Building ZINC000270268625 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270268625 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 192) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1) `ZINC000270268625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270268625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270268625 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 7, 7, 22, 22, 22, 22, 22, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 193) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1) `ZINC000270268625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270268625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270268625 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 6, 6, 26, 26, 26, 26, 26, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270268625 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270268625 Building ZINC000270324327 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270324327 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/194 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000270324327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270324327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270324327 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 33, 33, 33, 33, 33, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/195 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000270324327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270324327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270324327 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 33, 33, 33, 33, 33, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270324327 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 Building ZINC000270324327 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270324327 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 194) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000270324327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270324327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270324327 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 33, 33, 33, 33, 33, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 195) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1) `ZINC000270324327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270324327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000270324327 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 33, 33, 33, 33, 33, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270324327 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270324327 Building ZINC000270334774 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270334774 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/196 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1) `ZINC000270334774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270334774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000270334774 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 6, 6, 14, 22, 22, 22, 3, 3, 10, 10, 10, 10, 10, 3, 6, 6, 6, 14, 14, 22, 22, 22, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/197 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1) `ZINC000270334774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270334774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000270334774 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 6, 6, 14, 22, 22, 22, 3, 3, 9, 9, 9, 9, 9, 3, 6, 6, 6, 14, 14, 22, 22, 22, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270334774 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 Building ZINC000270334774 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270334774 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 196) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1) `ZINC000270334774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270334774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000270334774 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 2, 2, 6, 6, 14, 22, 22, 22, 3, 3, 10, 10, 10, 10, 10, 3, 6, 6, 6, 14, 14, 22, 22, 22, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 197) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1) `ZINC000270334774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270334774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000270334774 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 6, 6, 14, 22, 22, 22, 3, 3, 9, 9, 9, 9, 9, 3, 6, 6, 6, 14, 14, 22, 22, 22, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270334774 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270334774 Building ZINC000270342455 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270342455 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/198 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1) `ZINC000270342455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270342455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342455 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 11, 6, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 9, 9, 11, 11, 11, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/199 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1) `ZINC000270342455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270342455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342455 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 10, 6, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 9, 9, 10, 10, 10, 16, 16, 16, 7] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270342455 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 Building ZINC000270342455 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270342455 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 198) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1) `ZINC000270342455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270342455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342455 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 11, 6, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 9, 9, 11, 11, 11, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 199) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1) `ZINC000270342455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270342455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342455 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 10, 6, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 9, 9, 10, 10, 10, 16, 16, 16, 7] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270342455 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342455 Building ZINC000270342458 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270342458 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/200 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1) `ZINC000270342458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270342458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342458 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 9, 6, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 8, 8, 9, 9, 9, 16, 16, 16, 7] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/201 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1) `ZINC000270342458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270342458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342458 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 11, 6, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 9, 9, 11, 11, 11, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270342458 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 Building ZINC000270342458 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270342458 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 200) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1) `ZINC000270342458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270342458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342458 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 9, 6, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 8, 8, 9, 9, 9, 16, 16, 16, 7] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 201) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1) `ZINC000270342458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270342458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270342458 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(COC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 9, 11, 6, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 9, 9, 11, 11, 11, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270342458 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270342458 Building ZINC000270429948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270429948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/202 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1) `ZINC000270429948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270429948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429948 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 17, 17, 22, 22, 6, 6, 17, 17, 17, 17, 17, 6, 2, 14, 14, 51, 22, 22, 22, 22, 22, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/203 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1) `ZINC000270429948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270429948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429948 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 12, 12, 48, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270429948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 Building ZINC000270429948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270429948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 202) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1) `ZINC000270429948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270429948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429948 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 17, 17, 22, 22, 6, 6, 17, 17, 17, 17, 17, 6, 2, 14, 14, 51, 22, 22, 22, 22, 22, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 203) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1) `ZINC000270429948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270429948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429948 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 2, 12, 12, 48, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270429948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429948 Building ZINC000270429951 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270429951 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/204 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1) `ZINC000270429951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270429951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429951 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 15, 20, 20, 6, 6, 18, 18, 18, 18, 18, 6, 2, 12, 12, 48, 20, 20, 20, 20, 20, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/205 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1) `ZINC000270429951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270429951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429951 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 15, 20, 20, 5, 5, 14, 14, 14, 14, 14, 5, 2, 12, 12, 48, 20, 20, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270429951 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 Building ZINC000270429951 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270429951 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 204) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1) `ZINC000270429951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270429951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429951 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 15, 20, 20, 6, 6, 18, 18, 18, 18, 18, 6, 2, 12, 12, 48, 20, 20, 20, 20, 20, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 205) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1) `ZINC000270429951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270429951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000270429951 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 15, 20, 20, 5, 5, 14, 14, 14, 14, 14, 5, 2, 12, 12, 48, 20, 20, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270429951 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270429951 Building ZINC000270435986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270435986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/206 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1) `ZINC000270435986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270435986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270435986 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 12, 14, 20, 7, 7, 4, 4, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 12, 12, 14, 14, 20, 20, 20, 7, 7, 7, 7, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/207 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1) `ZINC000270435986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270435986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270435986 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 10, 12, 18, 7, 7, 5, 5, 15, 15, 15, 15, 15, 5, 7, 7, 7, 7, 10, 10, 12, 12, 18, 18, 18, 7, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270435986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 Building ZINC000270435986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270435986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 206) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1) `ZINC000270435986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270435986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270435986 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 12, 14, 20, 7, 7, 4, 4, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 12, 12, 14, 14, 20, 20, 20, 7, 7, 7, 7, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 207) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1) `ZINC000270435986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270435986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270435986 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCOC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 10, 12, 18, 7, 7, 5, 5, 15, 15, 15, 15, 15, 5, 7, 7, 7, 7, 10, 10, 12, 12, 18, 18, 18, 7, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270435986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270435986 Building ZINC000270441821 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441821 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/208 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/209 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/210 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/210' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/211 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/211' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441821 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 Building ZINC000270441821 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441821 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 208) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 209) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 210) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 211) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441821 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 Building ZINC000270441821 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441821 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 208) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 209) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 210) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 211) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441821 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 Building ZINC000270441821 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441821 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 208) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 209) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 210) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 25, 10, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 21, 21, 21, 21, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 211) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1) `ZINC000270441821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441821 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 20, 20, 25, 10, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 10, 10, 20, 20, 20, 20, 25, 25, 25, 10, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441821 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441821 Building ZINC000270441826 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441826 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/212 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/213 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/214 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/214' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/215 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/215' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441826 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 Building ZINC000270441826 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441826 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 212) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 213) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 214) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 215) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441826 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 Building ZINC000270441826 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441826 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 212) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 213) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 214) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 215) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441826 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 Building ZINC000270441826 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000270441826 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 212) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 213) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 214) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 18, 18, 20, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 11, 11, 18, 18, 18, 18, 20, 20, 20, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 215) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1) `ZINC000270441826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000270441826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000270441826 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 6, 12, 12, 12, 12, 12, 22, 22, 29, 12, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 12, 12, 22, 22, 22, 22, 29, 29, 29, 12, 12, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441826 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441826 Building ZINC000270441918 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270441918 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/216 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1) `ZINC000270441918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270441918 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 11, 14, 3, 7, 17, 17, 17, 3, 3, 7, 7, 7, 7, 7, 3, 8, 8, 11, 11, 14, 14, 14, 7, 7, 17, 17, 17, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/217 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1) `ZINC000270441918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270441918 none CCn1cc([C@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 11, 2, 4, 13, 13, 13, 3, 3, 6, 6, 6, 6, 6, 3, 5, 5, 6, 6, 11, 11, 11, 4, 4, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441918 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 Building ZINC000270441918 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270441918 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 216) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1) `ZINC000270441918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270441918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270441918 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 11, 14, 3, 7, 17, 17, 17, 3, 3, 7, 7, 7, 7, 7, 3, 8, 8, 11, 11, 14, 14, 14, 7, 7, 17, 17, 17, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 217) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1) `ZINC000270441918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270441918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000270441918 none CCn1cc([C@]([O-])([SiH3])C(=O)N(CCOC)CC(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 11, 2, 4, 13, 13, 13, 3, 3, 6, 6, 6, 6, 6, 3, 5, 5, 6, 6, 11, 11, 11, 4, 4, 13, 13, 13, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270441918 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270441918 Building ZINC000270558096 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270558096 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/218 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1) `ZINC000270558096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270558096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270558096 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 17, 17, 17, 10, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 10, 17, 17, 17, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/219 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1) `ZINC000270558096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270558096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270558096 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 16, 16, 16, 9, 6, 6, 18, 18, 18, 18, 18, 6, 2, 9, 9, 9, 16, 16, 16, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270558096 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 Building ZINC000270558096 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000270558096 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 218) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1) `ZINC000270558096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000270558096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270558096 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 17, 17, 17, 10, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 10, 17, 17, 17, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 219) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1) `ZINC000270558096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000270558096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000270558096 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2CN(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 16, 16, 16, 9, 6, 6, 18, 18, 18, 18, 18, 6, 2, 9, 9, 9, 16, 16, 16, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000270558096 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000270558096 Building ZINC000271893999 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271893999 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/220 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271893999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271893999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271893999 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 16, 16, 30, 30, 30, 27, 27, 12, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 48] 150 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]) total number of confs: 182 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/221 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271893999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271893999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271893999 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 30, 30, 30, 26, 26, 11, 11, 11, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 57] 150 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]) total number of confs: 203 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271893999 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 Building ZINC000271893999 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271893999 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 220) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271893999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271893999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271893999 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 16, 16, 30, 30, 30, 27, 27, 12, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 48] 150 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]) total number of confs: 182 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 221) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271893999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271893999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271893999 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 30, 30, 30, 26, 26, 11, 11, 11, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 57] 150 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]) total number of confs: 203 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271893999 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271893999 Building ZINC000271894001 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271894001 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/222 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271894001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271894001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271894001 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 27, 11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 18, 18, 31, 31, 31, 27, 27, 11, 11, 11, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 54] 150 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]) total number of confs: 201 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/223 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271894001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271894001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271894001 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 28, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 17, 17, 31, 31, 31, 28, 28, 12, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 51] 150 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]) total number of confs: 201 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271894001 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 Building ZINC000271894001 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271894001 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 222) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271894001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271894001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271894001 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 27, 11, 5, 11, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 18, 18, 31, 31, 31, 27, 27, 11, 11, 11, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 54] 150 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]) total number of confs: 201 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 223) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O) `ZINC000271894001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271894001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000271894001 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 28, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 17, 17, 31, 31, 31, 28, 28, 12, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 51] 150 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]) total number of confs: 201 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271894001 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271894001 Building ZINC000271965046 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271965046 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/224 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1) `ZINC000271965046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271965046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000271965046 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 44, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/225 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1) `ZINC000271965046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271965046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000271965046 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271965046 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 Building ZINC000271965046 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271965046 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 224) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1) `ZINC000271965046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271965046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000271965046 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 44, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 225) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1) `ZINC000271965046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271965046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000271965046 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCOCC1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271965046 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271965046 Building ZINC000271975871 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271975871 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/226 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271975871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271975871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000271975871 none COC(=O)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.3', '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, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 33, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 15, 15, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/227 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271975871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271975871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000271975871 none COC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.3', '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, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 37, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 17, 17, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271975871 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 Building ZINC000271975871 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000271975871 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 226) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271975871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000271975871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000271975871 none COC(=O)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.3', '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, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 33, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 15, 15, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 227) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000271975871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000271975871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000271975871 none COC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.3', '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, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 37, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 17, 17, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000271975871 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000271975871 Building ZINC000272025230 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272025230 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/228 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000272025230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272025230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000272025230 none CCOCCOC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 10, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 26, 26, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/229 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000272025230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272025230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000272025230 none CCOCCOC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 25, 19, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 34, 34, 34, 34, 34, 25, 25, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272025230 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 Building ZINC000272025230 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272025230 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 228) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOCCOC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000272025230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272025230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000272025230 none CCOCCOC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 10, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 26, 26, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 229) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOCCOC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000272025230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272025230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000272025230 none CCOCCOC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 25, 19, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 34, 34, 34, 34, 34, 25, 25, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272025230 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272025230 Building ZINC000272537922 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537922 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/230 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537922 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 15, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/231 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537922 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537922 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 Building ZINC000272537922 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537922 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 230) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537922 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 15, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 231) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537922 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537922 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537922 Building ZINC000272537927 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537927 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/232 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000272537927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537927 none C[C@@H]1CN[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 4, 16, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/233 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000272537927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537927 none C[C@@H]1CN[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 17, 4, 17, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537927 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 Building ZINC000272537927 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537927 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 232) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000272537927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537927 none C[C@@H]1CN[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 4, 16, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 233) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000272537927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537927 none C[C@@H]1CN[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 17, 4, 17, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537927 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537927 Building ZINC000272537930 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537930 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/234 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537930 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 10, 2, 10, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14] 40 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/235 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537930 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20] 47 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537930 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 Building ZINC000272537930 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537930 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 234) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537930 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 10, 2, 10, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14] 40 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 235) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1) `ZINC000272537930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537930 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20] 47 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537930 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537930 Building ZINC000272537935 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537935 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/236 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1) `ZINC000272537935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537935 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 13, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 48 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/237 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1) `ZINC000272537935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537935 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537935 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 Building ZINC000272537935 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272537935 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 236) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1) `ZINC000272537935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272537935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537935 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 13, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 48 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 237) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1) `ZINC000272537935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272537935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000272537935 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 1, 14, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272537935 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272537935 Building ZINC000272622084 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272622084 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/238 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000272622084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272622084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000272622084 none CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 24, 24, 24, 10, 2, 17, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 5, 5, 5, 5, 5, 24, 24] 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]) total number of confs: 93 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/239 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000272622084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272622084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000272622084 none CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 24, 24, 24, 10, 2, 16, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 24, 24, 24, 24, 5, 5, 5, 5, 5, 24, 24] 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]) total number of confs: 97 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272622084 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 Building ZINC000272622084 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272622084 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 238) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000272622084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272622084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000272622084 none CC(C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 24, 24, 24, 10, 2, 17, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 5, 5, 5, 5, 5, 24, 24] 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]) total number of confs: 93 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 239) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000272622084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272622084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000272622084 none CC(C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 24, 24, 24, 10, 2, 16, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 24, 24, 24, 24, 5, 5, 5, 5, 5, 24, 24] 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]) total number of confs: 97 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272622084 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272622084 Building ZINC000272648365 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272648365 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/240 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272648365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648365 none COC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 25, 38, 38, 38, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/241 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272648365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648365 none COC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 21, 11, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 29, 41, 41, 41, 38, 38, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272648365 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 Building ZINC000272648365 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272648365 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 240) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272648365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648365 none COC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 25, 38, 38, 38, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 241) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272648365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648365 none COC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 21, 11, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 29, 41, 41, 41, 38, 38, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272648365 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648365 Building ZINC000272648367 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272648367 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/242 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272648367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648367 none COC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 22, 12, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 31, 41, 41, 41, 38, 38, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/243 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272648367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648367 none COC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 18, 10, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 25, 37, 37, 37, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272648367 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 Building ZINC000272648367 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272648367 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 242) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272648367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648367 none COC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 22, 12, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 31, 41, 41, 41, 38, 38, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 243) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000272648367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272648367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000272648367 none COC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 18, 10, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 25, 37, 37, 37, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272648367 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272648367 Building ZINC000272920258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000272920258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/244 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/245 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/246 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/246' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/247 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/247' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272920258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 Building ZINC000272920258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000272920258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 244) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 245) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 246) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 247) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272920258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 Building ZINC000272920258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000272920258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 244) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 245) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 246) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 247) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272920258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 Building ZINC000272920258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000272920258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 244) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 245) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 246) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 247) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1) `ZINC000272920258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000272920258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000272920258 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCNC(=O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 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, 14, 26, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 18, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272920258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272920258 Building ZINC000272969730 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272969730 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/248 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1) `ZINC000272969730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272969730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969730 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 20, 29, 11, 19, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 20, 20, 29, 29, 29, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/249 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1) `ZINC000272969730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272969730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969730 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 27, 11, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 8, 8, 17, 17, 27, 27, 27, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272969730 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 Building ZINC000272969730 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272969730 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 248) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1) `ZINC000272969730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272969730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969730 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 20, 29, 11, 19, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 20, 20, 29, 29, 29, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 249) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1) `ZINC000272969730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272969730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969730 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 27, 11, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 8, 8, 17, 17, 27, 27, 27, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272969730 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969730 Building ZINC000272969732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272969732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/250 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1) `ZINC000272969732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272969732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969732 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 27, 11, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 8, 8, 17, 17, 27, 27, 27, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/251 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1) `ZINC000272969732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272969732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969732 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 20, 28, 11, 19, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 20, 20, 28, 28, 28, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272969732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 Building ZINC000272969732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000272969732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 250) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1) `ZINC000272969732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000272969732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969732 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 27, 11, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 8, 8, 17, 17, 27, 27, 27, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 251) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1) `ZINC000272969732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000272969732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000272969732 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](COC)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 20, 28, 11, 19, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 20, 20, 28, 28, 28, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000272969732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000272969732 Building ZINC000273009767 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273009767 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/252 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1) `ZINC000273009767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273009767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000273009767 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 42, 42, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/253 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1) `ZINC000273009767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273009767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000273009767 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 42, 42, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273009767 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 Building ZINC000273009767 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273009767 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 252) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1) `ZINC000273009767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273009767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000273009767 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 42, 42, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 253) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1) `ZINC000273009767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273009767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000273009767 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 42, 42, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273009767 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273009767 Building ZINC000273120049 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273120049 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/254 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273120049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120049 none CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 21, 21, 21, 11, 1, 14, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/255 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273120049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120049 none CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 21, 21, 21, 12, 1, 15, 1, 1, 1, 2, 2, 2, 21, 21, 21, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273120049 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 Building ZINC000273120049 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273120049 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 254) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273120049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120049 none CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 21, 21, 21, 11, 1, 14, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 255) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273120049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120049 none CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 21, 21, 21, 12, 1, 15, 1, 1, 1, 2, 2, 2, 21, 21, 21, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273120049 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120049 Building ZINC000273120050 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273120050 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/256 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273120050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120050 none CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 19, 19, 19, 11, 2, 14, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/257 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273120050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120050 none CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 22, 22, 22, 12, 2, 15, 1, 1, 1, 2, 2, 2, 22, 22, 22, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22] 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]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273120050 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 Building ZINC000273120050 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273120050 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 256) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273120050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120050 none CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 19, 19, 19, 11, 2, 14, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 257) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000273120050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273120050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273120050 none CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 22, 22, 22, 12, 2, 15, 1, 1, 1, 2, 2, 2, 22, 22, 22, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22] 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]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273120050 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273120050 Building ZINC000273282147 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273282147 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/258 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1) `ZINC000273282147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273282147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273282147 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 14, 7, 7, 7, 2, 2, 6, 6, 6, 6, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/259 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1) `ZINC000273282147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273282147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273282147 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 16, 8, 8, 8, 2, 2, 6, 6, 6, 6, 6, 2, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273282147 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 Building ZINC000273282147 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273282147 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 258) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1) `ZINC000273282147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273282147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273282147 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 14, 7, 7, 7, 2, 2, 6, 6, 6, 6, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 259) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1) `ZINC000273282147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273282147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000273282147 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC)C(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 16, 8, 8, 8, 2, 2, 6, 6, 6, 6, 6, 2, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273282147 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273282147 Building ZINC000273318079 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273318079 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/260 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000273318079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273318079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273318079 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 8, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/261 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000273318079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273318079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273318079 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 13, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273318079 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 Building ZINC000273318079 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273318079 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 260) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000273318079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273318079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273318079 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 8, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 261) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O) `ZINC000273318079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273318079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273318079 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 13, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 6, 6, 6, 6, 6, 17, 17] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273318079 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273318079 Building ZINC000273494328 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273494328 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/262 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000273494328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273494328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000273494328 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 30, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 279 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/263 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000273494328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273494328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000273494328 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 4, 13, 13, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 26, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273494328 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 Building ZINC000273494328 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273494328 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 262) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000273494328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273494328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000273494328 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 30, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 279 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 263) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000273494328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273494328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000273494328 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 4, 13, 13, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 26, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273494328 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273494328 Building ZINC000273705898 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273705898 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/264 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000273705898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273705898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000273705898 none COC(=O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 14, 14, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/265 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000273705898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273705898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000273705898 none COC(=O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273705898 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 Building ZINC000273705898 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273705898 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 264) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000273705898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273705898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000273705898 none COC(=O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 14, 14, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 265) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000273705898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273705898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000273705898 none COC(=O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273705898 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273705898 Building ZINC000273900499 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273900499 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/266 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO) `ZINC000273900499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273900499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000273900499 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 24, 24, 24, 45, 49, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 45, 45, 49, 49, 147] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/267 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NCCO) `ZINC000273900499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273900499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000273900499 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 24, 24, 24, 45, 49, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 45, 45, 49, 49, 147] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273900499 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 Building ZINC000273900499 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273900499 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 266) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO) `ZINC000273900499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273900499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000273900499 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 24, 24, 24, 45, 49, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 45, 45, 49, 49, 147] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 267) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NCCO) `ZINC000273900499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273900499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000273900499 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 24, 24, 24, 45, 49, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 45, 45, 49, 49, 147] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273900499 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273900499 Building ZINC000273995680 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273995680 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/268 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1) `ZINC000273995680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273995680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273995680 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 8, 8, 21, 38, 38, 38, 50, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 21, 21, 114, 50, 50, 150, 2, 2] 450 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]) total number of confs: 506 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/269 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1) `ZINC000273995680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273995680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273995680 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 9, 9, 24, 40, 40, 40, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 24, 24, 120, 50, 50, 150, 3, 3] 450 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]) total number of confs: 494 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273995680 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 Building ZINC000273995680 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273995680 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 268) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1) `ZINC000273995680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273995680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273995680 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 8, 8, 21, 38, 38, 38, 50, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 21, 21, 114, 50, 50, 150, 2, 2] 450 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]) total number of confs: 506 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 269) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1) `ZINC000273995680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273995680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000273995680 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)CO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 9, 9, 24, 40, 40, 40, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 24, 24, 120, 50, 50, 150, 3, 3] 450 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]) total number of confs: 494 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000273995680 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000273995680 Building ZINC000274088419 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274088419 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/270 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274088419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274088419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274088419 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 19, 34, 5, 19, 19, 33, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 34, 34, 33, 33, 99, 5, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 291 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/271 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274088419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274088419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274088419 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 30, 30, 90, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 258 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274088419 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 Building ZINC000274088419 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274088419 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 270) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274088419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274088419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274088419 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 19, 34, 5, 19, 19, 33, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 34, 34, 33, 33, 99, 5, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 291 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 271) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274088419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274088419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274088419 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 30, 30, 90, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 258 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274088419 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274088419 Building ZINC000274092382 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274092382 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/272 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCC(N)=O) `ZINC000274092382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274092382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000274092382 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 22, 38, 45, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 22, 22, 45, 45, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/273 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCC(N)=O) `ZINC000274092382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274092382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000274092382 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 22, 38, 45, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 22, 22, 45, 45, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274092382 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 Building ZINC000274092382 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274092382 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 272) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCC(N)=O) `ZINC000274092382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274092382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000274092382 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 22, 38, 45, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 22, 22, 45, 45, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 273) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCC(N)=O) `ZINC000274092382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274092382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000274092382 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 22, 38, 45, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 22, 22, 45, 45, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274092382 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274092382 Building ZINC000274135954 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274135954 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/274 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274135954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274135954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274135954 none COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 35, 15, 15, 9, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 44, 44, 35, 35, 15, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/275 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274135954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274135954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274135954 none COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 35, 15, 15, 9, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 45, 45, 35, 35, 15, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274135954 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 Building ZINC000274135954 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274135954 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 274) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274135954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274135954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274135954 none COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 35, 15, 15, 9, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 44, 44, 35, 35, 15, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 275) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274135954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274135954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274135954 none COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 35, 15, 15, 9, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 45, 45, 35, 35, 15, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274135954 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274135954 Building ZINC000274218312 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274218312 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/276 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCC(N)=O) `ZINC000274218312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274218312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000274218312 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 22, 30, 43, 43, 6, 6, 6, 6, 6, 6, 6, 5, 22, 22, 30, 30, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/277 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCC(N)=O) `ZINC000274218312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274218312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000274218312 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 21, 29, 43, 43, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 29, 29, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274218312 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 Building ZINC000274218312 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274218312 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 276) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCC(N)=O) `ZINC000274218312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274218312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000274218312 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 22, 30, 43, 43, 6, 6, 6, 6, 6, 6, 6, 5, 22, 22, 30, 30, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 277) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCC(N)=O) `ZINC000274218312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274218312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000274218312 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 5, 21, 29, 43, 43, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 29, 29, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274218312 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274218312 Building ZINC000274272610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274272610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/278 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274272610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274272610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274272610 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 30, 30, 90, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 258 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/279 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274272610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274272610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274272610 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 19, 34, 5, 19, 19, 33, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 34, 34, 33, 33, 99, 5, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 291 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274272610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 Building ZINC000274272610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274272610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 278) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000274272610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274272610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274272610 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 30, 30, 90, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 258 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 279) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000274272610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274272610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000274272610 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 19, 34, 5, 19, 19, 33, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 34, 34, 33, 33, 99, 5, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 291 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274272610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274272610 Building ZINC000274282991 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274282991 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/280 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1) `ZINC000274282991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274282991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000274282991 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 10, 17, 30, 30, 30, 30, 30, 30, 11, 11, 11, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/281 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1) `ZINC000274282991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274282991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000274282991 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 10, 16, 26, 26, 26, 26, 26, 26, 10, 10, 10, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26] 42 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274282991 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 Building ZINC000274282991 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274282991 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 280) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1) `ZINC000274282991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274282991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000274282991 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 10, 17, 30, 30, 30, 30, 30, 30, 11, 11, 11, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 281) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1) `ZINC000274282991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274282991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000274282991 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 10, 16, 26, 26, 26, 26, 26, 26, 10, 10, 10, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26] 42 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274282991 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274282991 Building ZINC000274390234 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274390234 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/282 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000274390234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274390234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000274390234 none CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 8, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 27, 27, 27, 27, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 37]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/283 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000274390234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274390234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000274390234 none CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 9, 9, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274390234 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 Building ZINC000274390234 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274390234 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 282) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000274390234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274390234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000274390234 none CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 8, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 27, 27, 27, 27, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 37]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 283) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000274390234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274390234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000274390234 none CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 9, 9, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274390234 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274390234 Building ZINC000274501652 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274501652 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/284 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/285 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/286 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/286' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/287 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/287' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274501652 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 Building ZINC000274501652 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274501652 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 284) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 285) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 286) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 287) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274501652 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 Building ZINC000274501652 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274501652 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 284) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 285) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 286) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 287) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274501652 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 Building ZINC000274501652 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274501652 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 284) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 285) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 15, 24, 30, 32, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 32, 32, 96, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 286) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 287) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000274501652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274501652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274501652 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 17, 25, 31, 33, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 33, 33, 99, 17, 17, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274501652 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274501652 Building ZINC000274515396 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274515396 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/288 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274515396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515396 none CCOC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 16, 26, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 39, 39, 39, 39, 39, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/289 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274515396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515396 none CCOC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 25, 25, 16, 25, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 37, 37, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274515396 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 Building ZINC000274515396 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274515396 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 288) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274515396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515396 none CCOC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 16, 26, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 39, 39, 39, 39, 39, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 289) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274515396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515396 none CCOC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 25, 25, 16, 25, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 37, 37, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274515396 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515396 Building ZINC000274515399 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274515399 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/290 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274515399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515399 none CCOC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 16, 26, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 37, 37, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/291 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274515399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515399 none CCOC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 15, 26, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 15, 15, 15, 15, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274515399 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 Building ZINC000274515399 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274515399 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 290) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274515399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515399 none CCOC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 16, 26, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 37, 37, 16, 16, 16, 16, 2, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 291) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000274515399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274515399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000274515399 none CCOC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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] 0 hydrogens 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, 26, 26, 15, 26, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 15, 15, 15, 15, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000274515399 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000274515399 Building ZINC000275163943 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163943 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/292 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163943 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 13, 13, 13, 13, 5, 13, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 19, 27, 27, 27, 27, 27, 13, 13, 3, 7, 7, 7, 7, 7, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/293 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163943 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 19, 31, 31, 31, 31, 31, 14, 14, 3, 6, 6, 6, 6, 6, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163943 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 Building ZINC000275163943 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163943 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 292) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163943 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 13, 13, 13, 13, 5, 13, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 19, 27, 27, 27, 27, 27, 13, 13, 3, 7, 7, 7, 7, 7, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 293) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163943 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 19, 31, 31, 31, 31, 31, 14, 14, 3, 6, 6, 6, 6, 6, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163943 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163943 Building ZINC000275163944 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163944 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/294 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163944 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 23, 33, 33, 33, 33, 33, 15, 15, 4, 8, 8, 8, 8, 8, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/295 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163944 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 21, 29, 29, 29, 29, 29, 15, 15, 2, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163944 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 Building ZINC000275163944 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163944 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 294) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163944 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 23, 33, 33, 33, 33, 33, 15, 15, 4, 8, 8, 8, 8, 8, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 295) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163944 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 21, 29, 29, 29, 29, 29, 15, 15, 2, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163944 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163944 Building ZINC000275163946 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163946 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/296 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163946 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 24, 30, 30, 30, 30, 30, 15, 15, 4, 8, 8, 8, 8, 8, 24, 24, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/297 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163946 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 14, 14, 14, 14, 6, 13, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 22, 32, 32, 32, 32, 32, 14, 14, 4, 7, 7, 7, 7, 7, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163946 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 Building ZINC000275163946 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163946 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 296) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163946 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 15, 24, 30, 30, 30, 30, 30, 15, 15, 4, 8, 8, 8, 8, 8, 24, 24, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 297) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC) `ZINC000275163946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163946 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 14, 14, 14, 14, 6, 13, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 22, 32, 32, 32, 32, 32, 14, 14, 4, 7, 7, 7, 7, 7, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163946 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163946 Building ZINC000275163948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/298 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163948 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 20, 33, 33, 33, 33, 33, 17, 17, 4, 7, 7, 7, 7, 7, 20, 20, 20] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/299 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163948 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 21, 32, 32, 32, 32, 32, 16, 16, 3, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 Building ZINC000275163948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275163948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 298) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275163948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163948 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 20, 33, 33, 33, 33, 33, 17, 17, 4, 7, 7, 7, 7, 7, 20, 20, 20] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 299) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC) `ZINC000275163948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275163948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000275163948 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 21, 32, 32, 32, 32, 32, 16, 16, 3, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275163948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275163948 Building ZINC000275196271 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196271 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/300 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/301 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/302 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/302' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/303 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/303' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196271 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 Building ZINC000275196271 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196271 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 300) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 301) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 302) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 303) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196271 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 Building ZINC000275196271 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196271 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 300) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 301) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 302) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 303) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196271 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 Building ZINC000275196271 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196271 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 300) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 301) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 15, 15, 15, 15, 12, 2, 14, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 30, 30, 30, 90, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 302) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 303) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196271 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 15, 15, 15, 15, 11, 2, 13, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 28, 28, 28, 84, 19, 19, 15, 15, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196271 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196271 Building ZINC000275196273 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196273 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/304 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/305 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/306 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/306' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/307 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/307' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196273 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 Building ZINC000275196273 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196273 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 304) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 305) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 306) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 307) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196273 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 Building ZINC000275196273 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196273 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 304) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 305) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 306) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 307) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196273 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 Building ZINC000275196273 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196273 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 304) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 305) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 28, 28, 28, 84, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 306) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 307) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1) `ZINC000275196273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196273 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 90, 20, 20, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196273 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196273 Building ZINC000275196274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/308 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/309 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/310 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/310' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/311 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/311' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 Building ZINC000275196274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 308) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 309) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 310) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 311) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 Building ZINC000275196274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 308) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 309) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 310) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 311) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 Building ZINC000275196274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 308) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 309) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 26, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 78, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 310) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 311) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196274.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196274 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 30, 30, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 30, 30, 30, 90, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196274 Building ZINC000275196275 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196275 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/312 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/313 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/314 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/314' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/315 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/315' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196275 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 Building ZINC000275196275 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196275 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 312) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 313) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 314) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 315) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196275 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 Building ZINC000275196275 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196275 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 312) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 313) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 314) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 315) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196275 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 Building ZINC000275196275 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275196275 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 312) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 313) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 78, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 314) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 315) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1) `ZINC000275196275.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275196275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000275196275 none C[C@@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 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, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 30, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 10, 30, 30, 30, 90, 18, 18, 10, 10, 10, 10, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275196275 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275196275 Building ZINC000275273980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275273980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/316 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/317 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 29, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/318 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/318' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 27, 27, 27, 27, 27, 27, 27, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/319 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/319' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 22, 22, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275273980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 Building ZINC000275273980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275273980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 316) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 317) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 29, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 318) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 27, 27, 27, 27, 27, 27, 27, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 319) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 22, 22, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275273980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 Building ZINC000275273980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275273980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 316) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 317) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 29, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 318) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 27, 27, 27, 27, 27, 27, 27, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 319) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 22, 22, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275273980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 Building ZINC000275273980 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000275273980 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 316) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 23, 23, 7, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 317) grep: /scratch/xiaobo/121205/xcw-8058088.75/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)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 29, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 318) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 27, 27, 27, 27, 27, 27, 27, 23, 23, 4, 10, 10, 10, 10, 10, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 319) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000275273980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000275273980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000275273980 none CC(C)[N@]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 22, 22, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 90 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275273980 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275273980 Building ZINC000275560927 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275560927 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/320 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)cn1) `ZINC000275560927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275560927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000275560927 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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, 5, 5, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 6, 17, 17, 17, 34, 34, 34, 17, 5, 5, 5, 5, 5, 5, 17, 17, 17, 34, 34, 34, 34, 34, 34, 102, 17, 17, 5] 150 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]) total number of confs: 213 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/321 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)cn1) `ZINC000275560927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275560927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000275560927 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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, 5, 5, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 6, 18, 18, 18, 36, 36, 36, 18, 5, 5, 5, 5, 5, 5, 18, 18, 18, 36, 36, 36, 36, 36, 36, 108, 18, 18, 5] 150 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]) total number of confs: 221 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275560927 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 Building ZINC000275560927 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275560927 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 320) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)cn1) `ZINC000275560927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275560927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000275560927 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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, 5, 5, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 6, 17, 17, 17, 34, 34, 34, 17, 5, 5, 5, 5, 5, 5, 17, 17, 17, 34, 34, 34, 34, 34, 34, 102, 17, 17, 5] 150 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]) total number of confs: 213 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 321) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)cn1) `ZINC000275560927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275560927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000275560927 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(C)(C)O)C2)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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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, 5, 5, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 6, 18, 18, 18, 36, 36, 36, 18, 5, 5, 5, 5, 5, 5, 18, 18, 18, 36, 36, 36, 36, 36, 36, 108, 18, 18, 5] 150 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]) total number of confs: 221 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275560927 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275560927 Building ZINC000275909622 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275909622 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/322 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000275909622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275909622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000275909622 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 16, 41, 41, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 16, 16, 16, 16, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/323 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000275909622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275909622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000275909622 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 43, 17, 43, 43, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275909622 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 Building ZINC000275909622 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275909622 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 322) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000275909622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275909622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000275909622 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 16, 41, 41, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 16, 16, 16, 16, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 323) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000275909622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275909622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000275909622 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 43, 17, 43, 43, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000275909622 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000275909622 Building ZINC000276324803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276324803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/324 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000276324803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276324803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000276324803 none CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 27, 27, 27, 27, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/325 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000276324803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276324803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000276324803 none CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 29, 29, 29, 29, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000276324803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 Building ZINC000276324803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276324803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 324) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000276324803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276324803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000276324803 none CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 27, 27, 27, 27, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 325) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000276324803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276324803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000276324803 none CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 29, 29, 29, 29, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000276324803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000276324803 Building ZINC000277508034 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508034 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/326 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508034 none C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 22, 22, 22] 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]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/327 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508034 none C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 13, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17] 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]) total number of confs: 47 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508034 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 Building ZINC000277508034 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508034 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 326) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508034 none C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 22, 22, 22] 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]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 327) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508034 none C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 13, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 17, 17, 17] 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]) total number of confs: 47 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508034 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508034 Building ZINC000277508036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/328 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)NCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277508036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000277508036 none C[C@@H]1[C@H](C)NCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11] 49 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/329 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C)NCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277508036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000277508036 none C[C@@H]1[C@H](C)NCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 Building ZINC000277508036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 328) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1[C@H](C)NCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277508036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000277508036 none C[C@@H]1[C@H](C)NCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11] 49 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 329) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@@H]1[C@H](C)NCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277508036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000277508036 none C[C@@H]1[C@H](C)NCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508036 Building ZINC000277508037 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508037 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/330 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508037 none C[C@@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 13, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 19, 19, 19] 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]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/331 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508037 none C[C@@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 14, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 19, 19, 19] 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]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508037 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 Building ZINC000277508037 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508037 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 330) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508037 none C[C@@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 13, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 19, 19, 19] 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]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 331) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C) `ZINC000277508037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508037 none C[C@@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 14, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 19, 19, 19] 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]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508037 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508037 Building ZINC000277508039 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508039 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/332 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000277508039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508039 none C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 19, 19, 19] 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]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/333 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000277508039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508039 none C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 3, 16, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 22, 22, 22] 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508039 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 Building ZINC000277508039 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277508039 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 332) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000277508039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277508039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508039 none C[C@H]1NCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 19, 19, 19] 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]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 333) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C) `ZINC000277508039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277508039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000277508039 none C[C@H]1NCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 3, 16, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 22, 22, 22] 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277508039 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277508039 Building ZINC000277705036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277705036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/334 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/334' -> `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)N1CC(C)(O)C1) `ZINC000277705036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277705036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000277705036 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 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, 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] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 54, 18, 18] 69 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/335 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/335' -> `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)N1CC(C)(O)C1) `ZINC000277705036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277705036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000277705036 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 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, 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] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 51, 17, 17] 63 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277705036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 Building ZINC000277705036 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277705036 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 334) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(O)C1) `ZINC000277705036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277705036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000277705036 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 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, 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] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 54, 18, 18] 69 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 335) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(O)C1) `ZINC000277705036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277705036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000277705036 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 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, 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] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 51, 17, 17] 63 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277705036 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277705036 Building ZINC000277747558 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277747558 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/336 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1) `ZINC000277747558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277747558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000277747558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 14, 8, 8, 8, 13, 8, 5, 5, 20, 20, 20, 20, 20, 5, 8, 8, 14, 14, 14, 13, 13, 13, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/337 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1) `ZINC000277747558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277747558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000277747558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 14, 9, 9, 9, 13, 9, 4, 4, 13, 13, 13, 13, 13, 4, 9, 9, 14, 14, 14, 13, 13, 13, 9, 9, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277747558 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 Building ZINC000277747558 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277747558 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 336) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1) `ZINC000277747558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277747558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000277747558 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 14, 8, 8, 8, 13, 8, 5, 5, 20, 20, 20, 20, 20, 5, 8, 8, 14, 14, 14, 13, 13, 13, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 337) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1) `ZINC000277747558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277747558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000277747558 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](OC)[C@@H](OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 14, 9, 9, 9, 13, 9, 4, 4, 13, 13, 13, 13, 13, 4, 9, 9, 14, 14, 14, 13, 13, 13, 9, 9, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277747558 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277747558 Building ZINC000277856987 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277856987 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/338 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1) `ZINC000277856987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277856987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000277856987 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 13, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9, 9, 9, 9, 3, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 31, 31, 31, 31, 9] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/339 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1) `ZINC000277856987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277856987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000277856987 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 3, 3, 3, 13, 31, 35, 35, 35, 35, 35, 31, 31, 8, 8, 8, 8, 8, 8, 3, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 31, 31, 8] 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277856987 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 Building ZINC000277856987 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277856987 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 338) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1) `ZINC000277856987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277856987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000277856987 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 13, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9, 9, 9, 9, 3, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 31, 31, 31, 31, 9] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 339) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1) `ZINC000277856987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277856987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000277856987 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(N3CCOCC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 3, 3, 3, 13, 31, 35, 35, 35, 35, 35, 31, 31, 8, 8, 8, 8, 8, 8, 3, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 31, 31, 8] 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277856987 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277856987 Building ZINC000277975152 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277975152 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/340 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC) `ZINC000277975152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277975152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000277975152 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 28, 23, 23, 23, 15, 15, 6, 6, 6, 6, 6, 15, 15, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/341 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC) `ZINC000277975152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277975152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000277975152 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 30, 26, 26, 26, 20, 20, 6, 6, 6, 6, 6, 20, 20, 30, 30, 30] 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277975152 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 Building ZINC000277975152 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277975152 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 340) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC) `ZINC000277975152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277975152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000277975152 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 28, 23, 23, 23, 15, 15, 6, 6, 6, 6, 6, 15, 15, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 341) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC) `ZINC000277975152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277975152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000277975152 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 30, 26, 26, 26, 20, 20, 6, 6, 6, 6, 6, 20, 20, 30, 30, 30] 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000277975152 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000277975152 Building ZINC000278770555 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278770555 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/342 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278770555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770555 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 33, 44, 44, 44, 44, 50, 50, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 44, 44, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/343 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278770555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770555 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 29, 46, 46, 46, 46, 50, 50, 46, 46, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 46, 46, 50, 50, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000278770555 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 Building ZINC000278770555 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278770555 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 342) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278770555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770555 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 33, 44, 44, 44, 44, 50, 50, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 44, 44, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 343) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278770555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770555 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 29, 46, 46, 46, 46, 50, 50, 46, 46, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 46, 46, 50, 50, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000278770555 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770555 Building ZINC000278770559 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278770559 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/344 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278770559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770559 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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, 1, 1, 1, 1, 5, 5, 5, 29, 46, 46, 46, 46, 49, 49, 46, 46, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 46, 46, 49, 49, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/345 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278770559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770559 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 33, 45, 45, 45, 45, 50, 50, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 45, 45, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000278770559 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 Building ZINC000278770559 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278770559 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 344) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278770559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770559 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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, 1, 1, 1, 1, 5, 5, 5, 29, 46, 46, 46, 46, 49, 49, 46, 46, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 46, 46, 49, 49, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 345) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1) `ZINC000278770559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278770559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000278770559 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 33, 45, 45, 45, 45, 50, 50, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 45, 45, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000278770559 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000278770559 Building ZINC000279431114 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279431114 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/346 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000279431114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279431114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000279431114 none NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 9, 6, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 12, 12, 9, 9, 9, 9, 6, 6, 5, 4, 4, 1, 4, 4] 14 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/347 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000279431114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279431114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000279431114 none NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 9, 6, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 11, 11, 9, 9, 9, 9, 6, 6, 5, 5, 5, 1, 5, 5] 14 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279431114 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 Building ZINC000279431114 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279431114 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 346) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000279431114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279431114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000279431114 none NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 9, 6, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 12, 12, 9, 9, 9, 9, 6, 6, 5, 4, 4, 1, 4, 4] 14 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 347) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000279431114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279431114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000279431114 none NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 9, 6, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 11, 11, 9, 9, 9, 9, 6, 6, 5, 5, 5, 1, 5, 5] 14 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279431114 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279431114 Building ZINC000279591690 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591690 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/348 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/348' -> `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)NC[C@@]1(O)CCO[C@H]1C) `ZINC000279591690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591690 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 28, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 138, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 283 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/349 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/349' -> `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)NC[C@@]1(O)CCO[C@H]1C) `ZINC000279591690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591690 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 29, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 123, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591690 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 Building ZINC000279591690 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591690 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 348) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000279591690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591690 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 28, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 138, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 283 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 349) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000279591690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591690 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 29, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 123, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591690 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591690 Building ZINC000279591697 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591697 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/350 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/350' -> `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)NC[C@]1(O)CCO[C@H]1C) `ZINC000279591697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591697 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 32, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 286 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/351 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/351' -> `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)NC[C@]1(O)CCO[C@H]1C) `ZINC000279591697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591697 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 28, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591697 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 Building ZINC000279591697 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591697 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 350) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000279591697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591697 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 32, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 286 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 351) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000279591697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591697 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 28, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591697 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591697 Building ZINC000279591703 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591703 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/352 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/352' -> `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)NC[C@]1(O)CCO[C@@H]1C) `ZINC000279591703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591703 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 126, 42, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/353 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/353' -> `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)NC[C@]1(O)CCO[C@@H]1C) `ZINC000279591703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591703 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 31, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591703 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 Building ZINC000279591703 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591703 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 352) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000279591703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591703 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 126, 42, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 353) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000279591703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591703 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 31, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 144, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591703 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591703 Building ZINC000279591710 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591710 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/354 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/354' -> `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)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000279591710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591710 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 296 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/355 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/355' -> `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)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000279591710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591710 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 32, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591710 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 Building ZINC000279591710 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279591710 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 354) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000279591710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279591710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591710 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 296 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 355) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000279591710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279591710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000279591710 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C 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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 32, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279591710 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279591710 Building ZINC000279600804 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600804 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/356 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600804 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 10, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 22, 22, 22, 22, 22, 27, 27, 27, 19, 19, 4, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/357 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600804 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 21, 21, 21, 21, 21, 26, 26, 26, 22, 22, 4, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600804 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 Building ZINC000279600804 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600804 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 356) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600804 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 10, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 22, 22, 22, 22, 22, 27, 27, 27, 19, 19, 4, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 357) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600804 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 21, 21, 21, 21, 21, 26, 26, 26, 22, 22, 4, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600804 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600804 Building ZINC000279600809 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600809 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/358 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600809 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 12, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 21, 21, 21, 21, 21, 33, 33, 33, 28, 28, 3, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/359 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600809 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 12, 4, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 21, 21, 21, 21, 21, 35, 35, 35, 27, 27, 4, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600809 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 Building ZINC000279600809 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600809 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 358) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600809 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 12, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 21, 21, 21, 21, 21, 33, 33, 33, 28, 28, 3, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 359) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600809 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 12, 4, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 21, 21, 21, 21, 21, 35, 35, 35, 27, 27, 4, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600809 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600809 Building ZINC000279600813 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600813 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/360 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600813 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 4, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/361 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600813 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 23, 23, 23, 23, 23, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600813 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 Building ZINC000279600813 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600813 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 360) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600813 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 4, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 361) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1) `ZINC000279600813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600813 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 4, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 23, 23, 23, 23, 23, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600813 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600813 Building ZINC000279600817 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600817 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/362 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600817 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 12, 4, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 21, 21, 21, 21, 21, 35, 35, 35, 27, 27, 4, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/363 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600817 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 12, 3, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 22, 22, 22, 22, 22, 34, 34, 34, 27, 27, 3, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600817 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 Building ZINC000279600817 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279600817 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 362) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279600817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600817 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 12, 4, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 21, 21, 21, 21, 21, 35, 35, 35, 27, 27, 4, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 363) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1) `ZINC000279600817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279600817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000279600817 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 12, 3, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 22, 22, 22, 22, 22, 34, 34, 34, 27, 27, 3, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279600817 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279600817 Building ZINC000279607534 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279607534 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/364 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)cn1) `ZINC000279607534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279607534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000279607534 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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, 9, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 6, 6, 6, 6, 6, 18, 30, 30, 6, 4, 4, 4, 4, 4, 4, 6, 6, 18, 18, 30, 30, 30, 30, 30, 6, 6, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/365 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)cn1) `ZINC000279607534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279607534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000279607534 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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, 9, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 7, 7, 7, 7, 7, 18, 29, 29, 7, 4, 4, 4, 4, 4, 4, 7, 7, 18, 18, 29, 29, 29, 29, 29, 7, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279607534 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 Building ZINC000279607534 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279607534 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 364) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)cn1) `ZINC000279607534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279607534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000279607534 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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, 9, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 6, 6, 6, 6, 6, 18, 30, 30, 6, 4, 4, 4, 4, 4, 4, 6, 6, 18, 18, 30, 30, 30, 30, 30, 6, 6, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 365) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)cn1) `ZINC000279607534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279607534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000279607534 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CC3CC3)C2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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, 9, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 7, 7, 7, 7, 7, 18, 29, 29, 7, 4, 4, 4, 4, 4, 4, 7, 7, 18, 18, 29, 29, 29, 29, 29, 7, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000279607534 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000279607534 Building ZINC000280053812 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280053812 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/366 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000280053812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280053812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000280053812 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 26, 26, 26, 12, 12, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/367 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000280053812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280053812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000280053812 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 13, 31, 31, 31, 13, 13, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280053812 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 Building ZINC000280053812 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280053812 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 366) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000280053812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280053812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000280053812 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 26, 26, 26, 12, 12, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 367) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C) `ZINC000280053812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280053812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000280053812 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 13, 31, 31, 31, 13, 13, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280053812 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280053812 Building ZINC000280161320 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161320 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/368 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161320 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 13, 33, 33, 33, 27, 27, 27, 4, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/369 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161320 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 15, 33, 33, 33, 29, 29, 29, 4, 4, 4, 4, 4, 4, 33, 33, 33, 99] 150 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]) total number of confs: 282 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161320 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 Building ZINC000280161320 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161320 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 368) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161320 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 13, 33, 33, 33, 27, 27, 27, 4, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 369) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161320 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 15, 33, 33, 33, 29, 29, 29, 4, 4, 4, 4, 4, 4, 33, 33, 33, 99] 150 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]) total number of confs: 282 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161320 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161320 Building ZINC000280161323 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161323 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/370 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161323 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 16, 34, 33, 34, 29, 29, 29, 5, 3, 3, 1, 3, 3, 34, 34, 34, 102] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 290 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/371 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161323 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 32, 31, 32, 29, 29, 29, 4, 3, 3, 1, 3, 3, 32, 32, 32, 96] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161323 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 Building ZINC000280161323 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161323 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 370) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161323 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 16, 34, 33, 34, 29, 29, 29, 5, 3, 3, 1, 3, 3, 34, 34, 34, 102] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 290 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 371) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O) `ZINC000280161323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161323 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 32, 31, 32, 29, 29, 29, 4, 3, 3, 1, 3, 3, 32, 32, 32, 96] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161323 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161323 Building ZINC000280161328 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161328 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/372 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161328 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 32, 31, 32, 29, 29, 29, 4, 3, 3, 1, 3, 3, 32, 32, 32, 96] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/373 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161328 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 15, 33, 32, 33, 29, 29, 29, 5, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 288 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161328 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 Building ZINC000280161328 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161328 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 372) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161328 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 32, 31, 32, 29, 29, 29, 4, 3, 3, 1, 3, 3, 32, 32, 32, 96] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 373) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161328 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 15, 33, 32, 33, 29, 29, 29, 5, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 288 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161328 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161328 Building ZINC000280161332 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161332 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/374 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161332 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 14, 28, 4, 14, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 14, 31, 31, 31, 28, 28, 28, 4, 4, 4, 1, 4, 4, 31, 31, 31, 93] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 275 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/375 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161332 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 13, 33, 33, 33, 27, 27, 27, 4, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161332 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 Building ZINC000280161332 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280161332 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 374) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280161332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161332 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 14, 28, 4, 14, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 14, 31, 31, 31, 28, 28, 28, 4, 4, 4, 1, 4, 4, 31, 31, 31, 93] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 275 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 375) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O) `ZINC000280161332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280161332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000280161332 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 13, 33, 33, 33, 27, 27, 27, 4, 3, 3, 1, 3, 3, 33, 33, 33, 99] 150 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280161332 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280161332 Building ZINC000280307897 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000280307897 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/376 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/377 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/378 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/378' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/379 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/379' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280307897 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 Building ZINC000280307897 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000280307897 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 376) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 377) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 378) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 379) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280307897 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 Building ZINC000280307897 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000280307897 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 376) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 377) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 378) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 379) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280307897 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 Building ZINC000280307897 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000280307897 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 376) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 377) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 378) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 2, 2, 2, 12, 19, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 12, 12, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 379) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCN2CC=CCC2)cn1) `ZINC000280307897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000280307897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000280307897 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CC=CCC2)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.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 13, 20, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 2, 13, 13, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280307897 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280307897 Building ZINC000280616352 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280616352 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/380 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280616352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616352 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 14, 25, 4, 14, 14, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 25, 29, 29, 87, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/381 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280616352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616352 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 13, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 32, 32, 96, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280616352 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 Building ZINC000280616352 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280616352 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 380) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280616352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616352 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 14, 25, 4, 14, 14, 29, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 25, 29, 29, 87, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 381) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280616352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616352 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 13, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 32, 32, 96, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280616352 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616352 Building ZINC000280616354 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280616354 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/382 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280616354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616354 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 13, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 32, 32, 96, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/383 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280616354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616354 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 14, 26, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 30, 30, 90, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280616354 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 Building ZINC000280616354 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280616354 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 382) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280616354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616354 none COC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 13, 27, 4, 13, 13, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 27, 27, 27, 32, 32, 96, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 383) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280616354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000280616354 none COC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 14, 26, 4, 14, 14, 30, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 26, 26, 26, 30, 30, 90, 4, 3, 3, 1, 3, 3] 150 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]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280616354 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280616354 Building ZINC000280686575 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280686575 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/384 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280686575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280686575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000280686575 none CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 33, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 33, 33, 21, 21, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/385 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280686575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280686575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000280686575 none CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 34, 22, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 34, 34, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280686575 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 Building ZINC000280686575 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280686575 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 384) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280686575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280686575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000280686575 none CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 33, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 33, 33, 21, 21, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 385) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280686575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280686575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000280686575 none CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 34, 22, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 34, 34, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280686575 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280686575 Building ZINC000280750047 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280750047 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/386 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1) `ZINC000280750047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280750047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280750047 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 43, 43, 20, 20, 5, 3, 3, 6, 3, 3, 34, 43, 43, 43, 43, 43] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/387 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1) `ZINC000280750047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280750047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280750047 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 43, 43, 20, 20, 5, 3, 3, 6, 3, 3, 34, 43, 43, 43, 43, 43] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280750047 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 Building ZINC000280750047 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280750047 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 386) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1) `ZINC000280750047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280750047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280750047 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 43, 43, 20, 20, 5, 3, 3, 6, 3, 3, 34, 43, 43, 43, 43, 43] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 387) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1) `ZINC000280750047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280750047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280750047 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 43, 43, 20, 20, 5, 3, 3, 6, 3, 3, 34, 43, 43, 43, 43, 43] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280750047 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280750047 Building ZINC000280847838 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280847838 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/388 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280847838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280847838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280847838 none O=C(N1CCNC(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 10, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 46 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/389 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280847838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280847838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280847838 none O=C(N1CCNC(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 10, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 46 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280847838 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 Building ZINC000280847838 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280847838 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 388) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280847838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280847838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280847838 none O=C(N1CCNC(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 10, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 46 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 389) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280847838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280847838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280847838 none O=C(N1CCNC(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 10, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 46 rigid atoms, others: [1, 10, 11, 12] set([0, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280847838 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280847838 Building ZINC000280893986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280893986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/390 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280893986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280893986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280893986 none CS(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 46, 48, 48, 23, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 46, 23, 23, 15, 15, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/391 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280893986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280893986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280893986 none CS(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 47, 48, 48, 26, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 47, 26, 26, 16, 16, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280893986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 Building ZINC000280893986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280893986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 390) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CS(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280893986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280893986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280893986 none CS(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 46, 48, 48, 23, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 46, 23, 23, 15, 15, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 391) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280893986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280893986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280893986 none CS(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 47, 48, 48, 26, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 47, 26, 26, 16, 16, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280893986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280893986 Building ZINC000280898959 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280898959 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/392 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280898959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280898959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000280898959 none O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 16, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 10, 5, 5] 52 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/393 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280898959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280898959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000280898959 none O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 14, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 48 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280898959 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 Building ZINC000280898959 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280898959 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 392) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280898959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280898959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000280898959 none O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 16, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 10, 5, 5] 52 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 393) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280898959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280898959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000280898959 none O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 14, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 10, 5, 5] 48 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280898959 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280898959 Building ZINC000280918118 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280918118 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/394 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000280918118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280918118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000280918118 none NS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 36, 36, 36, 8, 1, 13, 1, 1, 1, 2, 2, 1, 2, 2, 36, 36, 50, 50, 36, 36, 36, 36, 2, 2, 2, 2, 2, 36, 36, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/395 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000280918118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280918118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000280918118 none NS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 50, 50, 33, 33, 33, 7, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 33, 33, 50, 50, 33, 33, 33, 33, 3, 3, 1, 3, 3, 33, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280918118 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 Building ZINC000280918118 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280918118 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 394) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000280918118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280918118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000280918118 none NS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 36, 36, 36, 8, 1, 13, 1, 1, 1, 2, 2, 1, 2, 2, 36, 36, 50, 50, 36, 36, 36, 36, 2, 2, 2, 2, 2, 36, 36, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 395) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000280918118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280918118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000280918118 none NS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 50, 50, 33, 33, 33, 7, 1, 11, 1, 1, 1, 3, 3, 1, 3, 3, 33, 33, 50, 50, 33, 33, 33, 33, 3, 3, 1, 3, 3, 33, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280918118 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280918118 Building ZINC000280933421 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280933421 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/396 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280933421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933421 none O=C(N1CCO[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [15, 1, 15, 31, 31, 31, 31, 31, 31, 48, 31, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 48, 48, 144, 31, 31, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 298 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/397 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280933421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933421 none O=C(N1CCO[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [12, 1, 12, 29, 29, 29, 29, 29, 29, 48, 29, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 48, 48, 144, 29, 29, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 316 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280933421 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 Building ZINC000280933421 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280933421 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 396) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: O=C(N1CCO[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280933421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933421 none O=C(N1CCO[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [15, 1, 15, 31, 31, 31, 31, 31, 31, 48, 31, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 48, 48, 144, 31, 31, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 298 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 397) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280933421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933421 none O=C(N1CCO[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [12, 1, 12, 29, 29, 29, 29, 29, 29, 48, 29, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 48, 48, 144, 29, 29, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 316 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280933421 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933421 Building ZINC000280933423 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280933423 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/398 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280933423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933423 none O=C(N1CCO[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [9, 1, 15, 28, 28, 28, 28, 28, 28, 49, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 28, 49, 49, 147, 28, 28, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 324 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/399 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280933423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933423 none O=C(N1CCO[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 18, 30, 30, 30, 30, 30, 30, 46, 30, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 46, 46, 138, 30, 30, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280933423 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 Building ZINC000280933423 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280933423 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 398) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(N1CCO[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280933423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933423 none O=C(N1CCO[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [9, 1, 15, 28, 28, 28, 28, 28, 28, 49, 28, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 28, 49, 49, 147, 28, 28, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 324 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 399) grep: /scratch/xiaobo/121205/xcw-8058088.75/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(N1CCO[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280933423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280933423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000280933423 none O=C(N1CCO[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 18, 30, 30, 30, 30, 30, 30, 46, 30, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 46, 46, 138, 30, 30, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280933423 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280933423 Building ZINC000280937715 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937715 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/400 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937715 none C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 8, 4, 4] 28 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/401 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937715 none C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 11, 2, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 8, 4, 4] 32 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937715 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 Building ZINC000280937715 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937715 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 400) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937715 none C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 8, 4, 4] 28 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 401) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937715 none C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 11, 2, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 8, 4, 4] 32 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937715 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937715 Building ZINC000280937717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/402 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937717 none C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 10, 5, 5] 26 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/403 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937717 none C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 8, 4, 4] 20 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 Building ZINC000280937717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 402) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937717 none C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 10, 5, 5] 26 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 403) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000280937717 none C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 8, 4, 4] 20 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937717 Building ZINC000280937738 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937738 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/404 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937738 none O=C(N1CCN2C(=O)NC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 8, 4, 4] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/405 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937738 none O=C(N1CCN2C(=O)NC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 10, 5, 5] 62 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937738 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 Building ZINC000280937738 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937738 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 404) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937738 none O=C(N1CCN2C(=O)NC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 8, 4, 4] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 405) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937738 none O=C(N1CCN2C(=O)NC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 10, 5, 5] 62 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937738 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937738 Building ZINC000280937740 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937740 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/406 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937740 none O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10, 5, 5] 58 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/407 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937740 none O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 2, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 8, 4, 4] 46 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937740 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 Building ZINC000280937740 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280937740 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 406) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280937740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937740 none O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10, 5, 5] 58 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 407) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280937740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280937740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280937740 none O=C(N1CCN2C(=O)NC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 2, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 8, 4, 4] 46 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280937740 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280937740 Building ZINC000280961558 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961558 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/408 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961558 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 37, 37, 37, 27, 27, 27, 4, 3, 3, 6, 3, 3, 37, 37, 37, 111] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/409 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961558 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 38, 38, 38, 29, 29, 29, 5, 4, 4, 8, 4, 4, 38, 38, 38, 114] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961558 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 Building ZINC000280961558 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961558 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 408) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961558 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 37, 37, 37, 27, 27, 27, 4, 3, 3, 6, 3, 3, 37, 37, 37, 111] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 409) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961558 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 38, 38, 38, 29, 29, 29, 5, 4, 4, 8, 4, 4, 38, 38, 38, 114] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961558 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961558 Building ZINC000280961560 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961560 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/410 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961560 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 16, 27, 4, 16, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 32, 30, 32, 27, 27, 27, 4, 3, 3, 6, 3, 3, 32, 32, 32, 96] 300 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]) total number of confs: 281 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/411 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961560 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [31, 31, 15, 31, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 34, 34, 34, 31, 31, 31, 5, 3, 3, 6, 3, 3, 34, 34, 34, 102] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 305 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961560 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 Building ZINC000280961560 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961560 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 410) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961560 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 16, 27, 4, 16, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 32, 30, 32, 27, 27, 27, 4, 3, 3, 6, 3, 3, 32, 32, 32, 96] 300 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]) total number of confs: 281 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 411) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961560 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [31, 31, 15, 31, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 34, 34, 34, 31, 31, 31, 5, 3, 3, 6, 3, 3, 34, 34, 34, 102] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 305 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961560 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961560 Building ZINC000280961562 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961562 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/412 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961562 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [31, 31, 15, 31, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 34, 34, 34, 31, 31, 31, 5, 3, 3, 6, 3, 3, 34, 34, 34, 102] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 305 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/413 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961562 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 16, 27, 4, 16, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 32, 30, 32, 27, 27, 27, 4, 3, 3, 6, 3, 3, 32, 32, 32, 96] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 285 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961562 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 Building ZINC000280961562 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961562 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 412) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961562 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [31, 31, 15, 31, 5, 15, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 34, 34, 34, 31, 31, 31, 5, 3, 3, 6, 3, 3, 34, 34, 34, 102] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 305 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 413) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O) `ZINC000280961562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961562 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 16, 27, 4, 16, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 32, 30, 32, 27, 27, 27, 4, 3, 3, 6, 3, 3, 32, 32, 32, 96] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 285 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961562 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961562 Building ZINC000280961563 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961563 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/414 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961563 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 38, 38, 38, 29, 29, 29, 5, 4, 4, 8, 4, 4, 38, 38, 38, 114] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/415 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961563 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 37, 37, 37, 27, 27, 27, 4, 3, 3, 6, 3, 3, 37, 37, 37, 111] 300 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]) total number of confs: 313 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961563 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 Building ZINC000280961563 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280961563 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 414) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280961563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961563 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [29, 29, 16, 29, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 38, 38, 38, 29, 29, 29, 5, 4, 4, 8, 4, 4, 38, 38, 38, 114] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 415) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O) `ZINC000280961563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280961563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000280961563 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 27, 4, 13, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 37, 37, 37, 27, 27, 27, 4, 3, 3, 6, 3, 3, 37, 37, 37, 111] 300 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]) total number of confs: 313 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280961563 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280961563 Building ZINC000280978102 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280978102 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/416 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280978102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280978102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280978102 none O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 18, 28, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 3, 3, 2, 11, 11, 21, 21, 28, 28, 48, 48, 48, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/417 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280978102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280978102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280978102 none O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 18, 29, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 2, 11, 11, 21, 21, 29, 29, 49, 49, 49, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280978102 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 Building ZINC000280978102 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280978102 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 416) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000280978102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280978102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280978102 none O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 18, 28, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 1, 3, 3, 2, 11, 11, 21, 21, 28, 28, 48, 48, 48, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 417) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000280978102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280978102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000280978102 none O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 18, 29, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 2, 11, 11, 21, 21, 29, 29, 49, 49, 49, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000280978102 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000280978102 Building ZINC000281011288 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281011288 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/418 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281011288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281011288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000281011288 none COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 33, 16, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 33, 33, 16, 9, 9, 2, 3, 3, 6, 3, 3] 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/419 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281011288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281011288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000281011288 none COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 36, 18, 18, 11, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 36, 36, 18, 11, 11, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281011288 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 Building ZINC000281011288 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281011288 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 418) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281011288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281011288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000281011288 none COCCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 33, 16, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 33, 33, 16, 9, 9, 2, 3, 3, 6, 3, 3] 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 419) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281011288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281011288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000281011288 none COCCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 36, 18, 18, 11, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 36, 36, 18, 11, 11, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281011288 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011288 Building ZINC000281011292 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281011292 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/420 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000281011292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281011292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000281011292 none NC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 50, 17, 17, 17, 17, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 34, 34, 17, 17, 17, 17, 3, 3, 6, 3, 3, 17, 17, 17, 17] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/421 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000281011292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281011292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000281011292 none NC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 50, 15, 15, 15, 15, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 34, 34, 15, 15, 15, 15, 3, 3, 6, 3, 3, 15, 15, 15, 15] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281011292 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 Building ZINC000281011292 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281011292 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 420) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000281011292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281011292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000281011292 none NC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 50, 17, 17, 17, 17, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 34, 34, 17, 17, 17, 17, 3, 3, 6, 3, 3, 17, 17, 17, 17] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 421) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC000281011292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281011292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000281011292 none NC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 50, 15, 15, 15, 15, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 34, 34, 15, 15, 15, 15, 3, 3, 6, 3, 3, 15, 15, 15, 15] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281011292 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281011292 Building ZINC000281014481 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281014481 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/422 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000281014481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281014481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000281014481 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 18, 2, 27, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 10, 5, 5, 36, 36] 86 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/423 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000281014481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281014481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000281014481 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 18, 2, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34] 76 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281014481 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 Building ZINC000281014481 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281014481 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 422) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000281014481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281014481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000281014481 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 18, 2, 27, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 10, 5, 5, 36, 36] 86 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 423) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000281014481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281014481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000281014481 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 18, 2, 26, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34] 76 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281014481 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281014481 Building ZINC000281038399 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281038399 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/424 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1) `ZINC000281038399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281038399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281038399 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/425 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1) `ZINC000281038399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281038399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281038399 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281038399 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 Building ZINC000281038399 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281038399 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 424) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1) `ZINC000281038399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281038399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281038399 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 48, 48, 48, 48, 48, 17, 17, 4, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 425) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1) `ZINC000281038399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281038399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281038399 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281038399 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281038399 Building ZINC000281044000 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281044000 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/426 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281044000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281044000 none CN(C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 28, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 28, 28, 18, 18, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/427 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281044000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281044000 none CN(C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 28, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 28, 28, 18, 18, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281044000 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 Building ZINC000281044000 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281044000 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 426) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281044000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281044000 none CN(C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 28, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 28, 28, 18, 18, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 427) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN(C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281044000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000281044000 none CN(C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 28, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 28, 28, 18, 18, 3, 3, 3, 6, 3, 3] 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281044000 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044000 Building ZINC000281044499 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281044499 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/428 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281044499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000281044499 none CNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 34, 42, 24, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 42, 42, 42, 34, 34, 24, 24, 6, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/429 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281044499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000281044499 none CNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 34, 42, 24, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 42, 42, 42, 34, 34, 24, 24, 6, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281044499 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 Building ZINC000281044499 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281044499 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 428) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281044499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000281044499 none CNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 34, 42, 24, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 42, 42, 42, 34, 34, 24, 24, 6, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 429) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000281044499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281044499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000281044499 none CNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 34, 42, 24, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 42, 42, 42, 42, 34, 34, 24, 24, 6, 3, 3, 6, 3, 3] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281044499 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281044499 Building ZINC000281413837 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000281413837 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/430 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/431 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/432 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/432' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/433 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/433' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281413837 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 Building ZINC000281413837 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000281413837 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 430) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 431) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 432) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 433) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281413837 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 Building ZINC000281413837 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000281413837 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 430) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 431) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 432) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 433) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281413837 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 Building ZINC000281413837 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000281413837 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 430) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 431) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 432) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 14, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 17, 17, 17, 18, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 433) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000281413837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000281413837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000281413837 none O=C(NCCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 13, 27, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 16, 16, 17, 16, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281413837 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281413837 Building ZINC000281997302 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281997302 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/434 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1) `ZINC000281997302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281997302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 40, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 40, 40, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/435 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1) `ZINC000281997302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281997302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 34, 34, 34, 34, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 34, 34, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281997302 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 Building ZINC000281997302 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281997302 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 434) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1) `ZINC000281997302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281997302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 40, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 40, 40, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 435) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1) `ZINC000281997302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281997302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 34, 34, 34, 34, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 34, 34, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281997302 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997302 Building ZINC000281997305 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281997305 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/436 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1) `ZINC000281997305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281997305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997305 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 35, 35, 35, 35, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 35, 35, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/437 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1) `ZINC000281997305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281997305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997305 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 40, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 40, 40, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281997305 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 Building ZINC000281997305 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000281997305 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 436) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1) `ZINC000281997305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000281997305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997305 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 35, 35, 35, 35, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 35, 35, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 437) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1) `ZINC000281997305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000281997305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000281997305 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC(C(N)=O)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 40, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 40, 40, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000281997305 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000281997305 Building ZINC000282356601 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282356601 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/438 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1) `ZINC000282356601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282356601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000282356601 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 17, 19, 4, 2, 2, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 17, 17, 19, 19, 19, 4, 4, 2] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/439 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1) `ZINC000282356601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282356601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000282356601 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 17, 20, 4, 2, 2, 6, 6, 6, 6, 6, 2, 4, 4, 11, 11, 17, 17, 20, 20, 20, 4, 4, 2] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282356601 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 Building ZINC000282356601 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282356601 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 438) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1) `ZINC000282356601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282356601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000282356601 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 17, 19, 4, 2, 2, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 17, 17, 19, 19, 19, 4, 4, 2] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 439) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1) `ZINC000282356601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282356601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000282356601 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(CCOC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 17, 20, 4, 2, 2, 6, 6, 6, 6, 6, 2, 4, 4, 11, 11, 17, 17, 20, 20, 20, 4, 4, 2] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282356601 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282356601 Building ZINC000282375095 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282375095 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/440 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC000282375095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282375095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000282375095 none COCCN1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/441 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC000282375095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282375095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000282375095 none COCCN1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282375095 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 Building ZINC000282375095 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282375095 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 440) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC000282375095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282375095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000282375095 none COCCN1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 441) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCCN1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC000282375095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282375095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000282375095 none COCCN1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282375095 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282375095 Building ZINC000282436465 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282436465 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/442 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1) `ZINC000282436465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282436465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436465 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/443 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1) `ZINC000282436465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282436465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436465 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282436465 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 Building ZINC000282436465 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282436465 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 442) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1) `ZINC000282436465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282436465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436465 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 14, 14, 14, 14, 14, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 443) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1) `ZINC000282436465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282436465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436465 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282436465 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436465 Building ZINC000282436469 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282436469 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/444 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1) `ZINC000282436469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282436469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436469 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 7, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 17, 17, 17, 17, 17, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/445 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1) `ZINC000282436469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282436469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436469 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 8, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 13, 13, 13, 13, 13, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282436469 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 Building ZINC000282436469 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282436469 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 444) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1) `ZINC000282436469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282436469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436469 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 7, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 17, 17, 17, 17, 17, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 445) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1) `ZINC000282436469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282436469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282436469 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 8, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 13, 13, 13, 13, 13, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282436469 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282436469 Building ZINC000282788811 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282788811 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/446 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/446' -> `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)N1CC(=O)NCC1(C)C) `ZINC000282788811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282788811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000282788811 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 16 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/447 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/447' -> `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)N1CC(=O)NCC1(C)C) `ZINC000282788811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282788811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000282788811 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 16 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282788811 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 Building ZINC000282788811 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282788811 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 446) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C) `ZINC000282788811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282788811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000282788811 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 16 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 447) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C) `ZINC000282788811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282788811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000282788811 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)NCC1(C)C 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 16 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282788811 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282788811 Building ZINC000282796452 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282796452 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/448 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282796452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282796452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000282796452 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11] 42 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/449 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282796452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282796452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000282796452 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11] 42 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282796452 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 Building ZINC000282796452 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282796452 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 448) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282796452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282796452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000282796452 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11] 42 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 449) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282796452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282796452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000282796452 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11] 42 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]) total number of confs: 34 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282796452 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282796452 Building ZINC000282806210 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282806210 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/450 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)cn1) `ZINC000282806210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282806210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000282806210 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)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.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 12, 12, 27, 27, 27, 44, 44, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 44, 44, 44, 44, 44, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/451 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)cn1) `ZINC000282806210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282806210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000282806210 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)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.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 12, 12, 26, 26, 26, 43, 43, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 43, 43, 43, 43, 43, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282806210 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 Building ZINC000282806210 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282806210 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 450) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)cn1) `ZINC000282806210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282806210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000282806210 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)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.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 12, 12, 27, 27, 27, 44, 44, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 44, 44, 44, 44, 44, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 451) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)cn1) `ZINC000282806210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282806210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000282806210 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCOC(=O)C2CC2)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.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 12, 12, 26, 26, 26, 43, 43, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 43, 43, 43, 43, 43, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282806210 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282806210 Building ZINC000282814710 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282814710 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/452 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282814710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282814710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282814710 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 6, 10, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/453 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282814710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282814710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282814710 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 9, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282814710 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 Building ZINC000282814710 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282814710 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 452) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282814710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282814710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282814710 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 6, 10, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 453) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1) `ZINC000282814710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282814710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000282814710 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)NCC2(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 5, 9, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000282814710 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000282814710 Building ZINC000285911952 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000285911952 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/454 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1) `ZINC000285911952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000285911952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000285911952 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [37, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 12, 6, 14, 14, 14, 14, 14, 14, 12] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/455 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1) `ZINC000285911952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000285911952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000285911952 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [36, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 6, 6, 6, 12, 12, 36, 36, 36, 36, 36, 12, 6, 14, 14, 14, 14, 14, 14, 12] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000285911952 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 Building ZINC000285911952 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000285911952 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 454) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1) `ZINC000285911952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000285911952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000285911952 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [37, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 12, 6, 14, 14, 14, 14, 14, 14, 12] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 455) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1) `ZINC000285911952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000285911952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000285911952 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(N(C)C)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [36, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 6, 6, 6, 12, 12, 36, 36, 36, 36, 36, 12, 6, 14, 14, 14, 14, 14, 14, 12] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000285911952 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000285911952 Building ZINC000286179339 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286179339 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/456 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O) `ZINC000286179339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286179339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286179339 none CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 5, 8, 8, 15, 15, 15, 15, 15, 14, 14, 2, 6, 16, 16, 16, 16, 16, 6, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/457 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O) `ZINC000286179339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286179339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286179339 none CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 6, 7, 7, 17, 17, 17, 16, 17, 16, 16, 3, 6, 18, 18, 18, 18, 18, 6, 7, 7] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286179339 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 Building ZINC000286179339 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286179339 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 456) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O) `ZINC000286179339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286179339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286179339 none CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 5, 8, 8, 15, 15, 15, 15, 15, 14, 14, 2, 6, 16, 16, 16, 16, 16, 6, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 457) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O) `ZINC000286179339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286179339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286179339 none CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 6, 7, 7, 17, 17, 17, 16, 17, 16, 16, 3, 6, 18, 18, 18, 18, 18, 6, 7, 7] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286179339 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286179339 Building ZINC000286188353 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286188353 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/458 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/458' -> `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)CCC(N)=O) `ZINC000286188353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286188353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286188353 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 22, 31, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 22, 22, 31, 31, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/459 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/459' -> `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)CCC(N)=O) `ZINC000286188353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286188353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286188353 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 23, 32, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 23, 23, 32, 32, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286188353 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 Building ZINC000286188353 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286188353 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 458) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCC(N)=O) `ZINC000286188353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286188353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286188353 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 22, 31, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 22, 22, 31, 31, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 459) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCC(N)=O) `ZINC000286188353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286188353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000286188353 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 23, 32, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 23, 23, 32, 32, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286188353 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286188353 Building ZINC000286354005 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286354005 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/460 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O) `ZINC000286354005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286354005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000286354005 none CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 28, 28, 28, 28, 25, 25, 25, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/461 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O) `ZINC000286354005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286354005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000286354005 none CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 3, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 16, 16, 24, 24, 24, 23, 24, 20, 20, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286354005 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 Building ZINC000286354005 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286354005 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 460) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O) `ZINC000286354005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286354005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000286354005 none CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 28, 28, 28, 28, 25, 25, 25, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 461) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O) `ZINC000286354005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286354005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000286354005 none CCC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 3, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 16, 16, 24, 24, 24, 23, 24, 20, 20, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000286354005 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000286354005 Building ZINC000287062533 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287062533 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/462 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC000287062533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000287062533 none COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 40, 40, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 40, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/463 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC000287062533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000287062533 none COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 40, 40, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 40, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287062533 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 Building ZINC000287062533 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287062533 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 462) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC000287062533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000287062533 none COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 40, 40, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 40, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 463) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC000287062533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287062533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000287062533 none COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 40, 40, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 40, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287062533 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287062533 Building ZINC000287327252 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287327252 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/464 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287327252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327252 none CN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 13, 36, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 7, 6, 6, 12, 6, 6, 36, 36] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/465 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287327252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327252 none CN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 15, 34, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 8, 6, 6, 12, 6, 6, 34, 34] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287327252 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 Building ZINC000287327252 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287327252 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 464) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287327252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327252 none CN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 13, 36, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 7, 6, 6, 12, 6, 6, 36, 36] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 465) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287327252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327252 none CN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 15, 34, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 8, 6, 6, 12, 6, 6, 34, 34] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287327252 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327252 Building ZINC000287327254 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287327254 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/466 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287327254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327254 none CN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 14, 34, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 7, 6, 6, 12, 6, 6, 34, 34] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/467 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287327254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327254 none CN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 13, 39, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 7, 6, 6, 12, 6, 6, 39, 39] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287327254 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 Building ZINC000287327254 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287327254 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 466) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287327254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327254 none CN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 14, 34, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 7, 6, 6, 12, 6, 6, 34, 34] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 467) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287327254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287327254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287327254 none CN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 13, 39, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 39, 39, 39, 39, 39, 39, 39, 7, 6, 6, 12, 6, 6, 39, 39] 100 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287327254 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287327254 Building ZINC000287416438 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287416438 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/468 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O) `ZINC000287416438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287416438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000287416438 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [11, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 47, 47, 47, 47, 47, 47, 47, 11, 11, 11, 6, 6, 12, 6, 6, 47, 47, 47, 47, 141] 300 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/469 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O) `ZINC000287416438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287416438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000287416438 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [12, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 6, 6, 12, 6, 6, 46, 46, 46, 46, 138] 300 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 278 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287416438 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 Building ZINC000287416438 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287416438 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 468) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O) `ZINC000287416438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287416438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000287416438 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [11, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 47, 47, 47, 47, 47, 47, 47, 11, 11, 11, 6, 6, 12, 6, 6, 47, 47, 47, 47, 141] 300 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 469) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O) `ZINC000287416438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287416438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000287416438 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1COC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [12, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 6, 6, 12, 6, 6, 46, 46, 46, 46, 138] 300 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 278 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287416438 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287416438 Building ZINC000287500769 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287500769 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/470 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287500769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500769 none O=C(N[C@@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/471 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287500769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500769 none O=C(N[C@@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287500769 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 Building ZINC000287500769 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287500769 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 470) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287500769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500769 none O=C(N[C@@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 471) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287500769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500769 none O=C(N[C@@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287500769 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500769 Building ZINC000287500772 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287500772 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/472 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287500772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500772 none O=C(N[C@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 20, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/473 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287500772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500772 none O=C(N[C@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287500772 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 Building ZINC000287500772 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287500772 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 472) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287500772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500772 none O=C(N[C@H]1CCC(=O)NC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 20, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 473) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287500772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287500772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287500772 none O=C(N[C@H]1CCC(=O)NC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 6, 6, 12, 6, 6] 100 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287500772 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287500772 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/476' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/477' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/478' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/479' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/480' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/481' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 474) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 475) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 476) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 36, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 477) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 478) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 479) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 480) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 481) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628658.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628658 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628658 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/482 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/483 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/484' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/485' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/486' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/487' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/488' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/489' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287628661 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000287628661 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 482) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 483) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 484) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 485) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [49, 49, 49, 49, 49, 49, 34, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 3, 3, 3, 6, 3, 3, 49, 49] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `4' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 4 (index: 486) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `5' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 5 (index: 487) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `6' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 6 (index: 488) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `7' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 7 (index: 489) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287628661.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000287628661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000287628661 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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: [48, 48, 48, 48, 48, 48, 35, 48, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 3, 3, 3, 6, 3, 3, 48, 48] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287628661 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/0.* 6: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/6.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/2.* 4: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/4.* 5: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/5.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/3.* 7: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/7.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287628661 Building ZINC000287668526 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287668526 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/490 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287668526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287668526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000287668526 none CCN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 4, 8, 15, 30, 30, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 15, 15, 30, 30, 3, 3, 6, 3, 3] 70 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/491 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287668526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287668526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000287668526 none CCN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 4, 8, 15, 31, 31, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 15, 15, 31, 31, 3, 3, 6, 3, 3] 72 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287668526 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 Building ZINC000287668526 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287668526 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 490) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287668526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287668526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000287668526 none CCN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 4, 8, 15, 30, 30, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 15, 15, 30, 30, 3, 3, 6, 3, 3] 70 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 491) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287668526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287668526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000287668526 none CCN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 4, 8, 15, 31, 31, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 15, 15, 31, 31, 3, 3, 6, 3, 3] 72 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287668526 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287668526 Building ZINC000287686601 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287686601 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/492 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287686601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287686601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000287686601 none COCCN1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 29, 7, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 50, 50, 50, 49, 49, 29, 29, 7, 7, 2, 2, 4, 2, 2, 7, 7] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/493 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287686601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287686601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000287686601 none COCCN1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 28, 7, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 50, 50, 50, 49, 49, 28, 28, 7, 7, 2, 2, 4, 2, 2, 7, 7] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287686601 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 Building ZINC000287686601 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287686601 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 492) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287686601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287686601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000287686601 none COCCN1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 29, 7, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 50, 50, 50, 49, 49, 29, 29, 7, 7, 2, 2, 4, 2, 2, 7, 7] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 493) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000287686601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287686601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000287686601 none COCCN1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 28, 7, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 50, 50, 50, 49, 49, 28, 28, 7, 7, 2, 2, 4, 2, 2, 7, 7] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287686601 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287686601 Building ZINC000287723570 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287723570 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/494 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287723570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287723570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000287723570 none CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 14, 45, 14, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 45, 45, 45, 45, 14, 14, 14, 4, 4, 8, 4, 4, 14, 14] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/495 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287723570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287723570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000287723570 none CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 16, 46, 16, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 46, 46, 46, 46, 16, 16, 16, 5, 5, 10, 5, 5, 16, 16] 100 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287723570 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 Building ZINC000287723570 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287723570 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 494) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287723570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287723570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000287723570 none CNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 14, 45, 14, 14, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 45, 45, 45, 45, 14, 14, 14, 4, 4, 8, 4, 4, 14, 14] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 495) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287723570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287723570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000287723570 none CNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 16, 46, 16, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 46, 46, 46, 46, 16, 16, 16, 5, 5, 10, 5, 5, 16, 16] 100 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287723570 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287723570 Building ZINC000287767229 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287767229 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/496 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287767229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287767229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000287767229 none CNC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 36, 48, 15, 15, 15, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 50, 36, 15, 15, 15, 2, 2, 4, 2, 2, 15, 15] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/497 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287767229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287767229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000287767229 none CNC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 38, 48, 14, 14, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 50, 50, 50, 50, 38, 14, 14, 14, 2, 2, 4, 2, 2, 14, 14] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287767229 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 Building ZINC000287767229 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287767229 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 496) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287767229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287767229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000287767229 none CNC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 36, 48, 15, 15, 15, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 50, 36, 15, 15, 15, 2, 2, 4, 2, 2, 15, 15] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 497) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000287767229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287767229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000287767229 none CNC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 38, 48, 14, 14, 14, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 50, 50, 50, 50, 38, 14, 14, 14, 2, 2, 4, 2, 2, 14, 14] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287767229 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287767229 Building ZINC000287885465 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287885465 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/498 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287885465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287885465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287885465 none COC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 47, 31, 17, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 47, 47, 99, 17, 17, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 342 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/499 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287885465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287885465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287885465 none COC[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 45, 31, 17, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 45, 44, 99, 17, 17, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 333 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287885465 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 Building ZINC000287885465 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287885465 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 498) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287885465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287885465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287885465 none COC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 47, 31, 17, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 47, 47, 99, 17, 17, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 342 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 499) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287885465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287885465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000287885465 none COC[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 45, 31, 17, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 45, 44, 99, 17, 17, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 333 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000287885465 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000287885465 Building ZINC000288205253 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288205253 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/500 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288205253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288205253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288205253 none COC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 43, 31, 18, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 42, 43, 99, 18, 18, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 324 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/501 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288205253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288205253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288205253 none COC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 45, 31, 18, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 45, 45, 99, 18, 18, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 329 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288205253 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 Building ZINC000288205253 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288205253 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 500) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288205253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288205253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288205253 none COC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 43, 31, 18, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 42, 43, 99, 18, 18, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 324 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 501) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288205253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288205253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288205253 none COC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 45, 31, 18, 33, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 45, 45, 99, 18, 18, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 329 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288205253 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288205253 Building ZINC000288262389 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288262389 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/502 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000288262389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288262389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000288262389 none CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 17, 17, 17, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 17, 38, 38, 38, 38, 17, 17, 17, 5, 5, 10, 5, 5, 17, 17] 100 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/503 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000288262389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288262389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000288262389 none CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 19, 19, 19, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 19, 39, 39, 39, 39, 19, 19, 19, 5, 5, 10, 5, 5, 19, 19] 100 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288262389 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 Building ZINC000288262389 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288262389 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 502) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000288262389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288262389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000288262389 none CC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 17, 17, 17, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 17, 38, 38, 38, 38, 17, 17, 17, 5, 5, 10, 5, 5, 17, 17] 100 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 503) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000288262389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288262389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000288262389 none CC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 19, 19, 19, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 19, 39, 39, 39, 39, 19, 19, 19, 5, 5, 10, 5, 5, 19, 19] 100 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288262389 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288262389 Building ZINC000288320250 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288320250 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/504 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)OC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000288320250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288320250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000288320250 none CC(C)NC(=O)OC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 21, 16, 21, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 2, 2, 2, 2, 2, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/505 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)OC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000288320250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288320250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000288320250 none CC(C)NC(=O)OC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 19, 10, 19, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288320250 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 Building ZINC000288320250 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288320250 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 504) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)OC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000288320250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288320250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000288320250 none CC(C)NC(=O)OC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 21, 16, 21, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 2, 2, 2, 2, 2, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 505) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)OC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000288320250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288320250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000288320250 none CC(C)NC(=O)OC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 19, 10, 19, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288320250 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288320250 Building ZINC000288325236 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288325236 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/506 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288325236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325236 none COC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 35, 15, 4, 15, 15, 31, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 35, 35, 31, 31, 93, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/507 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288325236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325236 none COC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 33, 16, 3, 16, 16, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 33, 33, 33, 33, 99, 3, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 347 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288325236 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 Building ZINC000288325236 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288325236 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 506) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288325236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325236 none COC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 35, 15, 4, 15, 15, 31, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 35, 35, 31, 31, 93, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 507) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288325236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325236 none COC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 33, 16, 3, 16, 16, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 33, 33, 33, 33, 99, 3, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 347 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288325236 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325236 Building ZINC000288325240 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288325240 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/508 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288325240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325240 none COC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 35, 16, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 35, 35, 33, 33, 99, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 351 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/509 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288325240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325240 none COC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 35, 15, 4, 15, 15, 31, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 35, 35, 31, 31, 93, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288325240 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 Building ZINC000288325240 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288325240 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 508) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288325240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325240 none COC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 35, 16, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 35, 35, 33, 33, 99, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 351 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 509) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288325240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288325240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288325240 none COC[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 35, 15, 4, 15, 15, 31, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 35, 35, 31, 31, 93, 4, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288325240 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288325240 Building ZINC000288357803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288357803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/510 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288357803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357803 none O=C(NC[C@@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/511 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288357803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357803 none O=C(NC[C@@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 26, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288357803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 Building ZINC000288357803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288357803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 510) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288357803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357803 none O=C(NC[C@@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 511) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288357803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357803 none O=C(NC[C@@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 26, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288357803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357803 Building ZINC000288357806 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288357806 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/512 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288357806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357806 none O=C(NC[C@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 27, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 27, 27, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/513 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288357806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357806 none O=C(NC[C@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288357806 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 Building ZINC000288357806 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288357806 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 512) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288357806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357806 none O=C(NC[C@H]1CN2CCN1CC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 27, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 27, 27, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 513) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288357806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288357806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000288357806 none O=C(NC[C@H]1CN2CCN1CC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 10, 5, 5] 100 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288357806 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288357806 Building ZINC000288387776 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288387776 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/514 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)cn1) `ZINC000288387776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288387776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387776 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 28, 14, 30, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 4, 28, 28, 84, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 150 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]) total number of confs: 281 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/515 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)cn1) `ZINC000288387776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288387776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387776 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 15, 24, 15, 36, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 4, 24, 24, 72, 31, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 150 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]) total number of confs: 267 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288387776 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 Building ZINC000288387776 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288387776 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 514) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)cn1) `ZINC000288387776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288387776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387776 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 28, 14, 30, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 4, 28, 28, 84, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 150 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]) total number of confs: 281 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 515) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)cn1) `ZINC000288387776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288387776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387776 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 15, 24, 15, 36, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 4, 24, 24, 72, 31, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 150 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]) total number of confs: 267 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288387776 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387776 Building ZINC000288387789 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288387789 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/516 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)cn1) `ZINC000288387789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288387789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387789 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 16, 16, 25, 16, 36, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 4, 25, 25, 75, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6] 150 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]) total number of confs: 275 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/517 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)cn1) `ZINC000288387789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288387789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387789 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 28, 14, 31, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 4, 28, 28, 84, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 150 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]) total number of confs: 283 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288387789 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 Building ZINC000288387789 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288387789 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 516) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)cn1) `ZINC000288387789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288387789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387789 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 16, 16, 25, 16, 36, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 4, 25, 25, 75, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6] 150 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]) total number of confs: 275 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 517) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)cn1) `ZINC000288387789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288387789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000288387789 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CN2CCCCC2)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', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 28, 14, 31, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 4, 28, 28, 84, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 150 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]) total number of confs: 283 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288387789 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288387789 Building ZINC000288442596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000288442596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/518 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/519 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/520 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/520' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/521 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/521' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288442596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 Building ZINC000288442596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000288442596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 518) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 519) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 520) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 521) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288442596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 Building ZINC000288442596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000288442596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 518) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 519) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 520) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 521) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288442596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 Building ZINC000288442596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000288442596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 518) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 519) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 520) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 521) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288442596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000288442596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000288442596 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 4, 2, 2] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288442596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288442596 Building ZINC000288980161 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288980161 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/522 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288980161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288980161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288980161 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 40, 16, 40, 40, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 16, 16, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/523 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288980161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288980161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288980161 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 41, 16, 41, 41, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 16, 16, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288980161 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 Building ZINC000288980161 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288980161 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 522) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288980161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288980161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288980161 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 40, 16, 40, 40, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 16, 16, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 523) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288980161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288980161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000288980161 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 41, 16, 41, 41, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 16, 16, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000288980161 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000288980161 Building ZINC000289067830 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289067830 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/524 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289067830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067830 none NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 24, 47, 24, 24, 24, 24, 4, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 47, 47, 24, 24, 24, 24, 4, 4, 8, 4, 4, 24, 24] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 132 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/525 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289067830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067830 none NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 23, 43, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 43, 43, 23, 23, 23, 23, 4, 4, 8, 4, 4, 23, 23] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289067830 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 Building ZINC000289067830 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289067830 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 524) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289067830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067830 none NC(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 24, 47, 24, 24, 24, 24, 4, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 47, 47, 24, 24, 24, 24, 4, 4, 8, 4, 4, 24, 24] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 132 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 525) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289067830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067830 none NC(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 23, 43, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 43, 43, 23, 23, 23, 23, 4, 4, 8, 4, 4, 23, 23] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289067830 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067830 Building ZINC000289067835 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289067835 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/526 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289067835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067835 none NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 46, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 46, 46, 23, 23, 23, 23, 3, 3, 6, 3, 3, 23, 23] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/527 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289067835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067835 none NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 25, 48, 25, 25, 25, 25, 5, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 48, 48, 25, 25, 25, 25, 4, 4, 8, 4, 4, 25, 25] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289067835 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 Building ZINC000289067835 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289067835 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 526) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289067835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067835 none NC(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 46, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 46, 46, 23, 23, 23, 23, 3, 3, 6, 3, 3, 23, 23] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 527) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000289067835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289067835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000289067835 none NC(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 25, 48, 25, 25, 25, 25, 5, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 48, 48, 25, 25, 25, 25, 4, 4, 8, 4, 4, 25, 25] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289067835 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289067835 Building ZINC000289113430 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289113430 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/528 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289113430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000289113430 none CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 16, 26, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 16, 16, 8, 8, 8, 2, 2, 4, 2, 2] 52 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/529 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289113430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000289113430 none CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 13, 24, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 13, 13, 7, 7, 7, 2, 2, 4, 2, 2] 48 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289113430 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 Building ZINC000289113430 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289113430 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 528) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289113430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000289113430 none CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 16, 26, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 16, 16, 8, 8, 8, 2, 2, 4, 2, 2] 52 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 529) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289113430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000289113430 none CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 13, 24, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 13, 13, 7, 7, 7, 2, 2, 4, 2, 2] 48 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000289113430 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000289113430 Building ZINC000290717993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000290717993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/530 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/531 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/532 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/532' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/533 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/533' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000290717993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 Building ZINC000290717993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000290717993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 530) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 531) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 532) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 533) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000290717993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 Building ZINC000290717993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000290717993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 530) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 531) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 532) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 533) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000290717993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 Building ZINC000290717993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000290717993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 530) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 531) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 532) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 47, 36, 30, 20, 30, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 30, 30, 30, 20, 20, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 533) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000290717993.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000290717993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000290717993 none CN(C)CCN(C)CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 28, 19, 28, 17, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 28, 28, 28, 19, 19, 19, 19, 13, 13, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000290717993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000290717993 Building ZINC000291213008 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291213008 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/534 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291213008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291213008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291213008 none COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 19, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 24, 24, 19, 19, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/535 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291213008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291213008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291213008 none COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 16, 16, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291213008 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 Building ZINC000291213008 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291213008 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 534) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291213008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291213008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291213008 none COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 19, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 24, 24, 19, 19, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 535) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291213008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291213008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291213008 none COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 16, 16, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291213008 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291213008 Building ZINC000291214135 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291214135 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/536 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291214135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291214135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291214135 none COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 24, 24, 15, 15, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/537 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291214135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291214135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291214135 none COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 19, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 24, 24, 19, 19, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291214135 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 Building ZINC000291214135 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291214135 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 536) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291214135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291214135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291214135 none COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 24, 24, 15, 15, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 537) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000291214135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291214135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000291214135 none COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 19, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 24, 24, 19, 19, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291214135 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291214135 Building ZINC000291646754 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291646754 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/538 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000291646754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291646754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000291646754 none CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 45, 19, 37, 37, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 5, 3, 3, 1, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/539 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000291646754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291646754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000291646754 none CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 45, 19, 37, 37, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 5, 3, 3, 1, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291646754 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 Building ZINC000291646754 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291646754 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 538) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000291646754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291646754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000291646754 none CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 45, 19, 37, 37, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 5, 3, 3, 1, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 539) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000291646754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291646754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000291646754 none CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 45, 19, 37, 37, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 5, 3, 3, 1, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291646754 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291646754 Building ZINC000291999520 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291999520 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/540 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1) `ZINC000291999520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291999520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000291999520 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 13, 14, 14, 24, 24, 24, 4, 4, 9, 9, 9, 9, 9, 4, 2, 10, 10, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 72, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/541 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1) `ZINC000291999520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291999520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000291999520 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 14, 13, 14, 24, 24, 24, 4, 4, 8, 8, 8, 8, 8, 4, 2, 10, 10, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 72, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291999520 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 Building ZINC000291999520 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000291999520 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 540) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1) `ZINC000291999520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000291999520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000291999520 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 13, 14, 14, 24, 24, 24, 4, 4, 9, 9, 9, 9, 9, 4, 2, 10, 10, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 72, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 541) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1) `ZINC000291999520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000291999520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000291999520 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)OCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 14, 13, 14, 24, 24, 24, 4, 4, 8, 8, 8, 8, 8, 4, 2, 10, 10, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 72, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000291999520 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000291999520 Building ZINC000292397452 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292397452 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/542 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292397452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292397452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292397452 none COC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 30, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/543 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292397452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292397452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292397452 none COC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292397452 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 Building ZINC000292397452 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292397452 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 542) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292397452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292397452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292397452 none COC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 30, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 543) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292397452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292397452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292397452 none COC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292397452 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292397452 Building ZINC000292449663 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292449663 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/544 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292449663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292449663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292449663 none CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 16, 16, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/545 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292449663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292449663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292449663 none CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 16, 16, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292449663 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 Building ZINC000292449663 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292449663 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 544) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292449663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292449663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292449663 none CNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 16, 16, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 545) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000292449663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292449663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000292449663 none CNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 16, 16, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292449663 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292449663 Building ZINC000292473646 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292473646 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/546 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292473646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473646 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 26, 30, 30, 30, 28, 28, 28, 15, 15, 2, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/547 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292473646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473646 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 31, 31, 31, 30, 30, 30, 14, 14, 3, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292473646 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 Building ZINC000292473646 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292473646 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 546) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292473646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473646 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 26, 30, 30, 30, 28, 28, 28, 15, 15, 2, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 547) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292473646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473646 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 31, 31, 31, 30, 30, 30, 14, 14, 3, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292473646 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473646 Building ZINC000292473669 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292473669 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/548 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292473669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473669 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 31, 32, 32, 30, 30, 30, 15, 15, 3, 7, 7, 7, 7, 7, 31, 31, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/549 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292473669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473669 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 30, 30, 30, 28, 28, 28, 15, 15, 2, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292473669 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 Building ZINC000292473669 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292473669 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 548) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292473669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473669 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 30, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 31, 32, 32, 30, 30, 30, 15, 15, 3, 7, 7, 7, 7, 7, 31, 31, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 549) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C) `ZINC000292473669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292473669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000292473669 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 10, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 27, 30, 30, 30, 28, 28, 28, 15, 15, 2, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292473669 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292473669 Building ZINC000292735072 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292735072 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/550 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1) `ZINC000292735072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292735072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000292735072 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 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: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 17, 6, 6, 16, 16, 16, 16, 16, 6, 3, 14, 14, 14, 14, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/551 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1) `ZINC000292735072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292735072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000292735072 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 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: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 13, 13, 13, 13, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292735072 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 Building ZINC000292735072 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292735072 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 550) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1) `ZINC000292735072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292735072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000292735072 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 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: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 17, 6, 6, 16, 16, 16, 16, 16, 6, 3, 14, 14, 14, 14, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 551) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1) `ZINC000292735072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292735072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000292735072 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2COC[C@@H]2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 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: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 13, 13, 13, 13, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292735072 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292735072 Building ZINC000292839029 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292839029 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/552 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1) `ZINC000292839029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292839029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000292839029 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1 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', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.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, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 26, 44, 44, 44, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 24, 22, 44, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/553 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1) `ZINC000292839029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292839029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000292839029 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1 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', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.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, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 26, 44, 44, 44, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 22, 24, 44, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292839029 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 Building ZINC000292839029 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000292839029 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 552) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1) `ZINC000292839029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000292839029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000292839029 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1 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', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.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, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 26, 44, 44, 44, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 24, 22, 44, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 553) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1) `ZINC000292839029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000292839029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000292839029 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCn1cc(CO)nn1 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', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.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, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 26, 44, 44, 44, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 22, 24, 44, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000292839029 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000292839029 Building ZINC000293797948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293797948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/554 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000293797948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293797948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000293797948 none CCNC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 13, 13, 17, 17, 17, 17, 17, 8, 3, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/555 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000293797948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293797948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000293797948 none CCNC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 6, 15, 15, 21, 21, 21, 21, 21, 10, 3, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293797948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 Building ZINC000293797948 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293797948 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 554) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000293797948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293797948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000293797948 none CCNC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 13, 13, 17, 17, 17, 17, 17, 8, 3, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 555) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000293797948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293797948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000293797948 none CCNC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 6, 15, 15, 21, 21, 21, 21, 21, 10, 3, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293797948 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293797948 Building ZINC000293801243 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293801243 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/556 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1) `ZINC000293801243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293801243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293801243 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 17, 23, 23, 23, 23, 23, 23, 24, 23, 5, 5, 12, 12, 12, 12, 12, 5, 2, 12, 12, 23, 23, 23, 23, 24, 24, 72, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/557 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1) `ZINC000293801243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293801243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293801243 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 21, 27, 27, 27, 27, 27, 27, 28, 27, 5, 5, 10, 10, 10, 10, 10, 5, 2, 13, 13, 27, 27, 27, 27, 28, 28, 84, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293801243 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 Building ZINC000293801243 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293801243 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 556) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1) `ZINC000293801243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293801243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293801243 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 17, 23, 23, 23, 23, 23, 23, 24, 23, 5, 5, 12, 12, 12, 12, 12, 5, 2, 12, 12, 23, 23, 23, 23, 24, 24, 72, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 557) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1) `ZINC000293801243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293801243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293801243 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](CO)O2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 21, 27, 27, 27, 27, 27, 27, 28, 27, 5, 5, 10, 10, 10, 10, 10, 5, 2, 13, 13, 27, 27, 27, 27, 28, 28, 84, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293801243 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293801243 Building ZINC000293915899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293915899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/558 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000293915899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293915899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293915899 none CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 8, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 25, 25, 25, 25, 25, 13, 11, 8, 8, 5, 5, 2, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/559 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000293915899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293915899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293915899 none CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 8, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 25, 25, 25, 25, 25, 13, 11, 8, 8, 5, 5, 2, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293915899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 Building ZINC000293915899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293915899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 558) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000293915899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293915899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293915899 none CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 8, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 25, 25, 25, 25, 25, 13, 11, 8, 8, 5, 5, 2, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 559) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000293915899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293915899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000293915899 none CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 8, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 25, 25, 25, 25, 25, 13, 11, 8, 8, 5, 5, 2, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293915899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293915899 Building ZINC000293953129 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293953129 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/560 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000293953129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293953129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000293953129 none CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 19, 19, 19, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 26, 19, 12, 12, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/561 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000293953129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293953129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000293953129 none CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 18, 18, 18, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38, 38, 26, 18, 12, 12, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293953129 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 Building ZINC000293953129 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293953129 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 560) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000293953129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293953129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000293953129 none CCNC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 19, 19, 19, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 26, 19, 12, 12, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 561) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000293953129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293953129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000293953129 none CCNC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 18, 18, 18, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38, 38, 26, 18, 12, 12, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000293953129 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000293953129 Building ZINC000294072254 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294072254 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/562 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294072254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072254 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 18, 32, 10, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 18, 21, 32, 32, 32, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/563 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294072254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072254 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 19, 34, 12, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 19, 23, 34, 34, 34, 12, 12, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 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: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294072254 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 Building ZINC000294072254 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294072254 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 562) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294072254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072254 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 18, 32, 10, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 18, 21, 32, 32, 32, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 563) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294072254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072254 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 19, 34, 12, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 19, 23, 34, 34, 34, 12, 12, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 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: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294072254 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072254 Building ZINC000294072257 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294072257 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/564 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294072257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072257 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 20, 35, 12, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 23, 35, 35, 35, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 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: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/565 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294072257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072257 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 19, 33, 11, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 19, 22, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294072257 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 Building ZINC000294072257 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294072257 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 564) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294072257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072257 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 20, 35, 12, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 23, 35, 35, 35, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 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: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 565) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC) `ZINC000294072257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294072257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000294072257 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 19, 33, 11, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 19, 22, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294072257 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294072257 Building ZINC000294103017 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294103017 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/566 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294103017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103017 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 31, 46, 18, 31, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 36, 46, 46, 46, 18, 18, 4, 3, 3, 6, 3, 3, 36, 36, 36] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/567 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294103017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103017 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 28, 47, 16, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 33, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3, 33, 33, 33] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294103017 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 Building ZINC000294103017 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294103017 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 566) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294103017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103017 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 31, 46, 18, 31, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 36, 46, 46, 46, 18, 18, 4, 3, 3, 6, 3, 3, 36, 36, 36] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 567) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294103017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103017 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 28, 47, 16, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 33, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3, 33, 33, 33] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294103017 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103017 Building ZINC000294103019 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294103019 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/568 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294103019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103019 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 29, 47, 16, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 32, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3, 32, 32, 32] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/569 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294103019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103019 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 31, 46, 18, 31, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 37, 46, 46, 46, 18, 18, 4, 3, 3, 6, 3, 3, 37, 37, 37] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294103019 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 Building ZINC000294103019 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294103019 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 568) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294103019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103019 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 29, 47, 16, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 32, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3, 32, 32, 32] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 569) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC) `ZINC000294103019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294103019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294103019 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 31, 46, 18, 31, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 37, 46, 46, 46, 18, 18, 4, 3, 3, 6, 3, 3, 37, 37, 37] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294103019 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294103019 Building ZINC000294176343 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294176343 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/570 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1) `ZINC000294176343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294176343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000294176343 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 12, 14, 17, 17, 17, 17, 17, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 14, 14, 14, 14, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/571 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1) `ZINC000294176343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294176343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000294176343 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 13, 16, 19, 19, 19, 19, 19, 6, 6, 13, 13, 13, 13, 13, 6, 2, 12, 12, 16, 16, 16, 16, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294176343 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 Building ZINC000294176343 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294176343 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 570) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1) `ZINC000294176343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294176343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000294176343 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 10, 12, 14, 17, 17, 17, 17, 17, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 14, 14, 14, 14, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 571) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1) `ZINC000294176343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294176343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000294176343 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCCc2cnn(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 13, 16, 19, 19, 19, 19, 19, 6, 6, 13, 13, 13, 13, 13, 6, 2, 12, 12, 16, 16, 16, 16, 19, 19, 19, 19, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294176343 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294176343 Building ZINC000294178596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294178596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/572 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/572' -> `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)N1CCCn2nnnc21) `ZINC000294178596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294178596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000294178596 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCn2nnnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', '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, 5, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/573 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/573' -> `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)N1CCCn2nnnc21) `ZINC000294178596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294178596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000294178596 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCn2nnnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', '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, 5, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294178596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 Building ZINC000294178596 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294178596 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 572) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCn2nnnc21) `ZINC000294178596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294178596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000294178596 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCn2nnnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', '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, 5, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 573) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCn2nnnc21) `ZINC000294178596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294178596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000294178596 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCn2nnnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', '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, 5, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 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: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294178596 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294178596 Building ZINC000294189428 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294189428 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/574 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294189428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189428 none CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 35, 27, 27, 27, 27, 7, 27, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 27, 35, 35, 35, 27, 27, 27, 27, 27, 27, 5, 3, 3, 3, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/575 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294189428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189428 none CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 35, 27, 27, 27, 27, 9, 27, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 27, 35, 35, 35, 27, 27, 27, 27, 27, 27, 5, 4, 4, 4, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294189428 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 Building ZINC000294189428 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294189428 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 574) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294189428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189428 none CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 35, 27, 27, 27, 27, 7, 27, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 27, 35, 35, 35, 27, 27, 27, 27, 27, 27, 5, 3, 3, 3, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 575) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294189428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189428 none CS(=O)(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 35, 27, 27, 27, 27, 9, 27, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 27, 35, 35, 35, 27, 27, 27, 27, 27, 27, 5, 4, 4, 4, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294189428 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189428 Building ZINC000294189429 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294189429 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/576 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294189429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189429 none CS(=O)(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 37, 37, 31, 31, 31, 31, 8, 31, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 31, 37, 37, 37, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/577 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294189429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189429 none CS(=O)(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 34, 34, 28, 28, 28, 28, 7, 28, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 34, 34, 34, 28, 28, 28, 28, 28, 28, 4, 5, 5, 5, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294189429 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 Building ZINC000294189429 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294189429 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 576) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294189429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189429 none CS(=O)(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 37, 37, 31, 31, 31, 31, 8, 31, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 31, 37, 37, 37, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 577) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1) `ZINC000294189429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294189429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294189429 none CS(=O)(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 34, 34, 28, 28, 28, 28, 7, 28, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 34, 34, 34, 28, 28, 28, 28, 28, 28, 4, 5, 5, 5, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294189429 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294189429 Building ZINC000294219461 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294219461 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/578 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1) `ZINC000294219461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294219461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219461 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 10, 10, 15, 10, 16, 16, 16, 5, 5, 13, 13, 13, 13, 13, 5, 2, 9, 9, 15, 15, 15, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/579 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1) `ZINC000294219461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294219461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219461 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 14, 10, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 2, 10, 10, 14, 14, 14, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294219461 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 Building ZINC000294219461 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294219461 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 578) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1) `ZINC000294219461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294219461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219461 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 10, 10, 15, 10, 16, 16, 16, 5, 5, 13, 13, 13, 13, 13, 5, 2, 9, 9, 15, 15, 15, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 579) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1) `ZINC000294219461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294219461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219461 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 14, 10, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 2, 10, 10, 14, 14, 14, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294219461 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219461 Building ZINC000294219464 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294219464 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/580 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1) `ZINC000294219464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294219464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219464 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 13, 10, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 6, 2, 10, 10, 13, 13, 13, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/581 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1) `ZINC000294219464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294219464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219464 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 11, 11, 16, 11, 17, 17, 17, 5, 5, 13, 13, 13, 13, 13, 5, 3, 10, 10, 16, 16, 16, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294219464 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 Building ZINC000294219464 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294219464 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 580) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1) `ZINC000294219464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294219464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219464 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 13, 10, 14, 14, 14, 6, 6, 13, 13, 13, 13, 13, 6, 2, 10, 10, 13, 13, 13, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 581) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1) `ZINC000294219464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294219464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000294219464 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OC)C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 5, 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: [13, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 11, 11, 16, 11, 17, 17, 17, 5, 5, 13, 13, 13, 13, 13, 5, 3, 10, 10, 16, 16, 16, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294219464 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294219464 Building ZINC000294220196 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294220196 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/582 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000294220196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000294220196 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 9, 15, 14, 15, 15, 15, 15, 15, 15, 6, 6, 23, 23, 23, 23, 23, 6, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/583 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000294220196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000294220196 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 6, 8, 14, 13, 14, 14, 14, 14, 14, 14, 7, 7, 24, 24, 24, 24, 24, 7, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294220196 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 Building ZINC000294220196 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294220196 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 582) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000294220196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000294220196 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 6, 9, 15, 14, 15, 15, 15, 15, 15, 15, 6, 6, 23, 23, 23, 23, 23, 6, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 583) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000294220196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000294220196 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 6, 8, 14, 13, 14, 14, 14, 14, 14, 14, 7, 7, 24, 24, 24, 24, 24, 7, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294220196 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294220196 Building ZINC000294474298 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294474298 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/584 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000294474298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294474298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000294474298 none CNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 22, 42, 6, 22, 22, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 42, 42, 42, 42, 22, 22, 22, 6, 5, 5, 10, 5, 5] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/585 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000294474298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294474298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000294474298 none CNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 17, 38, 6, 17, 17, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 17, 17, 17, 6, 6, 6, 12, 6, 6] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294474298 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 Building ZINC000294474298 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294474298 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 584) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000294474298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294474298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000294474298 none CNC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 22, 42, 6, 22, 22, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 42, 42, 42, 42, 22, 22, 22, 6, 5, 5, 10, 5, 5] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 585) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000294474298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294474298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000294474298 none CNC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 17, 38, 6, 17, 17, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 38, 38, 38, 38, 17, 17, 17, 6, 6, 6, 12, 6, 6] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294474298 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294474298 Building ZINC000294568713 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294568713 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/586 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O) `ZINC000294568713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294568713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568713 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 5, 5, 10, 5, 5, 44, 44, 44] 100 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/587 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O) `ZINC000294568713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294568713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568713 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 3, 3, 6, 3, 3, 28, 28, 28] 70 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294568713 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 Building ZINC000294568713 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294568713 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 586) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O) `ZINC000294568713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294568713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568713 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 18, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 5, 5, 10, 5, 5, 44, 44, 44] 100 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 587) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O) `ZINC000294568713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294568713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568713 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 3, 3, 6, 3, 3, 28, 28, 28] 70 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294568713 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568713 Building ZINC000294568717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294568717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/588 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000294568717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294568717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568717 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 3, 3, 6, 3, 3, 25, 25, 25] 64 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/589 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000294568717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294568717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568717 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 18, 42, 42, 42, 42, 42, 42, 42, 26, 26, 26, 26, 26, 5, 5, 10, 5, 5, 42, 42, 42] 100 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294568717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 Building ZINC000294568717 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294568717 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 588) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000294568717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294568717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568717 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 3, 3, 6, 3, 3, 25, 25, 25] 64 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 589) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O) `ZINC000294568717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294568717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000294568717 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)[C@@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 18, 42, 42, 42, 42, 42, 42, 42, 26, 26, 26, 26, 26, 5, 5, 10, 5, 5, 42, 42, 42] 100 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294568717 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294568717 Building ZINC000294619042 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294619042 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/590 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/590' -> `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)NC[C@H]1CC[C@@H](CO)O1) `ZINC000294619042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294619042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000294619042 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1 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', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 26, 45, 45, 45, 45, 45, 45, 47, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 45, 45, 45, 45, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/591 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/591' -> `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)NC[C@H]1CC[C@@H](CO)O1) `ZINC000294619042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294619042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000294619042 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1 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', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 32, 42, 42, 42, 42, 42, 42, 46, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 42, 42, 42, 42, 46, 46, 138] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294619042 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 Building ZINC000294619042 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000294619042 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 590) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1) `ZINC000294619042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000294619042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000294619042 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1 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', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 26, 45, 45, 45, 45, 45, 45, 47, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 45, 45, 45, 45, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 591) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1) `ZINC000294619042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000294619042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000294619042 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](CO)O1 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', 'H', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 32, 42, 42, 42, 42, 42, 42, 46, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 42, 42, 42, 42, 46, 46, 138] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000294619042 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000294619042 Building ZINC000295568993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295568993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/592 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000295568993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295568993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000295568993 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 47, 17, 17, 17, 17, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 49, 49, 49, 47, 47, 51, 17, 17, 3, 3, 6, 3, 3, 17, 17] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/593 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000295568993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295568993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000295568993 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 46, 18, 18, 18, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 46, 46, 54, 18, 18, 3, 3, 6, 3, 3, 18, 18] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000295568993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 Building ZINC000295568993 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295568993 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 592) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000295568993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295568993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000295568993 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 47, 17, 17, 17, 17, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 49, 49, 49, 47, 47, 51, 17, 17, 3, 3, 6, 3, 3, 17, 17] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 593) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000295568993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295568993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000295568993 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 46, 18, 18, 18, 18, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 46, 46, 54, 18, 18, 3, 3, 6, 3, 3, 18, 18] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000295568993 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000295568993 Building ZINC000296192401 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296192401 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/594 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296192401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192401 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 18, 2, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8, 4, 4, 28, 28, 28] 70 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/595 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296192401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192401 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 10, 5, 5, 33, 33, 33] 78 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000296192401 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 Building ZINC000296192401 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296192401 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 594) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296192401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192401 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 18, 2, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8, 4, 4, 28, 28, 28] 70 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 595) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296192401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192401 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 10, 5, 5, 33, 33, 33] 78 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000296192401 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192401 Building ZINC000296192406 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296192406 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/596 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296192406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192406 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 19, 2, 20, 1, 1, 1, 5, 5, 1, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34, 34] 84 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/597 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296192406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192406 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 18, 2, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8, 4, 4, 28, 28, 28] 68 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000296192406 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 Building ZINC000296192406 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296192406 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 596) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296192406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192406 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 19, 2, 20, 1, 1, 1, 5, 5, 1, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34, 34] 84 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 597) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1) `ZINC000296192406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296192406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000296192406 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 18, 2, 18, 1, 1, 1, 4, 4, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8, 4, 4, 28, 28, 28] 68 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000296192406 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000296192406 Building ZINC000297233133 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297233133 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/598 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000297233133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297233133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000297233133 none CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.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, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 50, 24, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 41, 24, 24, 15, 15, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/599 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000297233133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297233133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000297233133 none CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.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, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 50, 50, 24, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 42, 24, 24, 15, 15, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297233133 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 Building ZINC000297233133 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297233133 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 598) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000297233133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297233133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000297233133 none CN(C)S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.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, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 50, 24, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 41, 24, 24, 15, 15, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 599) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000297233133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297233133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000297233133 none CN(C)S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.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, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 50, 50, 24, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 42, 24, 24, 15, 15, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297233133 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297233133 Building ZINC000297371502 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297371502 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/600 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297371502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371502 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 31, 31, 31, 31, 31, 31, 31, 20, 20, 6, 10, 10, 10] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/601 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297371502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371502 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 36, 24, 24, 24, 24, 7, 24, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 36, 36, 36, 36, 36, 36, 36, 24, 24, 7, 10, 10, 10] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297371502 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 Building ZINC000297371502 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297371502 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 600) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297371502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371502 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 31, 31, 31, 31, 31, 31, 31, 20, 20, 6, 10, 10, 10] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 601) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297371502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371502 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 36, 24, 24, 24, 24, 7, 24, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 36, 36, 36, 36, 36, 36, 36, 24, 24, 7, 10, 10, 10] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297371502 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371502 Building ZINC000297371507 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297371507 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/602 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297371507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371507 none CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 39, 29, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 39, 39, 39, 39, 39, 39, 39, 29, 29, 6, 10, 10, 10] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/603 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297371507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371507 none CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 37, 29, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 37, 37, 37, 37, 37, 37, 37, 29, 29, 6, 10, 10, 10] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297371507 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 Building ZINC000297371507 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297371507 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 602) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297371507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371507 none CC(C)N1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 39, 29, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 39, 39, 39, 39, 39, 39, 39, 29, 29, 6, 10, 10, 10] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 603) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O) `ZINC000297371507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297371507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000297371507 none CC(C)N1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc[nH]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 37, 29, 29, 29, 29, 11, 29, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 37, 37, 37, 37, 37, 37, 37, 29, 29, 6, 10, 10, 10] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297371507 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297371507 Building ZINC000297529545 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297529545 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/604 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1=O) `ZINC000297529545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297529545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000297529545 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 1, 11, 7, 7, 7, 7, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 10, 10, 10, 7, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 44, 44, 44, 44, 44, 26, 26, 10, 10, 10, 10, 2, 2, 2, 10, 10] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/605 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1=O) `ZINC000297529545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297529545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000297529545 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 1, 11, 7, 7, 7, 7, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 9, 9, 9, 6, 2, 9, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 44, 44, 44, 44, 44, 25, 25, 9, 9, 9, 9, 3, 3, 3, 9, 9] 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297529545 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 Building ZINC000297529545 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000297529545 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 604) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1=O) `ZINC000297529545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000297529545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000297529545 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 1, 11, 7, 7, 7, 7, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 10, 10, 10, 7, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 44, 44, 44, 44, 44, 26, 26, 10, 10, 10, 10, 2, 2, 2, 10, 10] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 605) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1=O) `ZINC000297529545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000297529545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000297529545 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 1, 11, 7, 7, 7, 7, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 9, 9, 9, 6, 2, 9, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 44, 44, 44, 44, 44, 25, 25, 9, 9, 9, 9, 3, 3, 3, 9, 9] 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000297529545 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000297529545 Building ZINC000298089053 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298089053 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/606 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000298089053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298089053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298089053 none COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 6, 17, 17, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 17, 17, 17, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/607 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000298089053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298089053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298089053 none COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 4, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298089053 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 Building ZINC000298089053 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298089053 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 606) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000298089053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298089053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298089053 none COC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 6, 17, 17, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 17, 17, 17, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 607) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000298089053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298089053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298089053 none COC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 4, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298089053 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298089053 Building ZINC000298144969 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298144969 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/608 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000298144969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298144969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000298144969 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 4, 13, 13, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 26, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/609 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000298144969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298144969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000298144969 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 30, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 292 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298144969 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 Building ZINC000298144969 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298144969 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 608) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000298144969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298144969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000298144969 none COC(=O)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 4, 13, 13, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 26, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 281 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 609) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000298144969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298144969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000298144969 none COC(=O)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 30, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3, 3, 3, 3] 150 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]) total number of confs: 292 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298144969 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298144969 Building ZINC000298217161 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298217161 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/610 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1) `ZINC000298217161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298217161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000298217161 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 24, 47, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 24, 24, 47, 48, 48, 48, 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]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/611 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1) `ZINC000298217161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298217161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000298217161 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 25, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 25, 25, 48, 48, 48, 48, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298217161 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 Building ZINC000298217161 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298217161 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 610) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1) `ZINC000298217161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298217161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000298217161 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 24, 47, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 24, 24, 47, 48, 48, 48, 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]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 611) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1) `ZINC000298217161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298217161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000298217161 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 25, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 25, 25, 48, 48, 48, 48, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298217161 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298217161 Building ZINC000298443145 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298443145 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/612 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nncn1C) `ZINC000298443145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298443145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298443145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nncn1C 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/613 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nncn1C) `ZINC000298443145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298443145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298443145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nncn1C 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 27, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 27, 27, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298443145 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 Building ZINC000298443145 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000298443145 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 612) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nncn1C) `ZINC000298443145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000298443145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298443145 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nncn1C 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 613) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nncn1C) `ZINC000298443145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000298443145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000298443145 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nncn1C 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 27, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 27, 27, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000298443145 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000298443145 Building ZINC000299479519 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299479519 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/614 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1) `ZINC000299479519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299479519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000299479519 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 5, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 6, 9, 9, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 11, 11, 5, 5] 14 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/615 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1) `ZINC000299479519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299479519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000299479519 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 5, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 6, 9, 9, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 11, 11, 5, 5] 14 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299479519 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 Building ZINC000299479519 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299479519 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 614) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1) `ZINC000299479519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299479519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000299479519 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 5, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 6, 9, 9, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 11, 11, 5, 5] 14 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 615) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1) `ZINC000299479519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299479519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000299479519 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCCS(N)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 5, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 6, 9, 9, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 11, 11, 5, 5] 14 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299479519 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299479519 Building ZINC000299481044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000299481044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/616 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/617 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/618 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/618' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/619 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/619' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299481044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 Building ZINC000299481044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000299481044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 616) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 617) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 618) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 619) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299481044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 Building ZINC000299481044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000299481044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 616) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 617) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 618) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 619) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299481044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 Building ZINC000299481044 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000299481044 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 616) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 617) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 618) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28] 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]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 619) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1) `ZINC000299481044.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000299481044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000299481044 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 21, 21, 16, 16, 4, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299481044 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299481044 Building ZINC000299558872 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299558872 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/620 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299558872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299558872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299558872 none COC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/621 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299558872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299558872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299558872 none COC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299558872 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 Building ZINC000299558872 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299558872 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 620) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299558872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299558872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299558872 none COC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 621) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299558872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299558872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299558872 none COC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299558872 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299558872 Building ZINC000299590726 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299590726 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/622 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299590726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590726 none COC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 11, 25, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/623 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299590726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590726 none COC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 25, 13, 13, 13, 13, 13, 13, 9, 9, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299590726 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 Building ZINC000299590726 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299590726 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 622) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299590726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590726 none COC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 11, 25, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 623) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299590726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590726 none COC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 25, 13, 13, 13, 13, 13, 13, 9, 9, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299590726 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590726 Building ZINC000299590730 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299590730 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/624 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299590730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590730 none COC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 10, 25, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 25, 10, 10, 10, 10, 10, 10, 9, 9, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/625 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299590730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590730 none COC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 11, 25, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299590730 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 Building ZINC000299590730 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299590730 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 624) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299590730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590730 none COC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 10, 25, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 25, 10, 10, 10, 10, 10, 10, 9, 9, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 625) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299590730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299590730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000299590730 none COC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 11, 25, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299590730 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299590730 Building ZINC000299606162 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299606162 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/626 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299606162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299606162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299606162 none CCOC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 33, 9, 33, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 9, 9, 6, 6, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/627 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299606162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299606162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299606162 none CCOC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 9, 34, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 9, 9, 6, 6, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299606162 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 Building ZINC000299606162 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299606162 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 626) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299606162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299606162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299606162 none CCOC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 33, 9, 33, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 9, 9, 6, 6, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 627) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCOC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000299606162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299606162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000299606162 none CCOC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 34, 34, 9, 34, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 9, 9, 6, 6, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299606162 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299606162 Building ZINC000299725603 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299725603 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/628 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/628' -> `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@@H]1CC(=O)N(C)C1) `ZINC000299725603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299725603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725603 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/629 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/629' -> `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@@H]1CC(=O)N(C)C1) `ZINC000299725603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299725603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725603 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299725603 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 Building ZINC000299725603 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299725603 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 628) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1) `ZINC000299725603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299725603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725603 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 629) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1) `ZINC000299725603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299725603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725603 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299725603 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725603 Building ZINC000299725604 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299725604 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/630 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/630' -> `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@H]1CC(=O)N(C)C1) `ZINC000299725604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299725604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725604 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/631 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/631' -> `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@H]1CC(=O)N(C)C1) `ZINC000299725604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299725604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725604 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299725604 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 Building ZINC000299725604 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000299725604 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 630) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1) `ZINC000299725604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000299725604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725604 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 631) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1) `ZINC000299725604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000299725604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000299725604 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000299725604 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000299725604 Building ZINC000330390062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/632 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/633 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/634 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/634' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/635 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/635' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 Building ZINC000330390062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 632) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 633) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 634) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 635) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 Building ZINC000330390062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 632) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 633) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 634) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 635) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 Building ZINC000330390062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 632) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 633) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 634) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 17, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 2, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 635) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(C)CCO2)cn1) `ZINC000330390062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390062 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390062 Building ZINC000330390067 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390067 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/636 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/637 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/638 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/638' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/639 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/639' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390067 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 Building ZINC000330390067 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390067 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 636) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 637) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 638) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 639) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390067 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 Building ZINC000330390067 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390067 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 636) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 637) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 638) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 639) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390067 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 Building ZINC000330390067 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330390067 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 636) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 637) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 638) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 20, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 639) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(C)CCO2)cn1) `ZINC000330390067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330390067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330390067 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C)CCO2)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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 10, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 6, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330390067 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330390067 Building ZINC000330410876 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330410876 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/640 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 33, 33, 33, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/641 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 33, 33, 33, 23, 23, 23, 23, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 13, 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/642 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/642' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 34, 34, 34, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/643 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/643' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 23, 23, 23, 23, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330410876 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 Building ZINC000330410876 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330410876 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 640) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 33, 33, 33, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 641) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 33, 33, 33, 23, 23, 23, 23, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 13, 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 642) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 34, 34, 34, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 643) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 23, 23, 23, 23, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330410876 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 Building ZINC000330410876 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330410876 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 640) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 33, 33, 33, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 641) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 33, 33, 33, 23, 23, 23, 23, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 13, 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 642) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 34, 34, 34, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 643) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 23, 23, 23, 23, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330410876 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 Building ZINC000330410876 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330410876 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 640) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 33, 33, 33, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 641) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 33, 33, 33, 23, 23, 23, 23, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 13, 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 642) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 24, 24, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 34, 34, 34, 24, 24, 24, 24, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 14, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 643) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000330410876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330410876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330410876 none COCC[N@]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 23, 23, 23, 23, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330410876 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330410876 Building ZINC000330419495 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330419495 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/644 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330419495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419495 none CNC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/645 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330419495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419495 none CNC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330419495 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 Building ZINC000330419495 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330419495 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 644) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330419495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419495 none CNC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 645) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CNC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330419495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419495 none CNC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330419495 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419495 Building ZINC000330419496 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330419496 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/646 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330419496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419496 none CNC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/647 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330419496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419496 none CNC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 12, 29, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330419496 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 Building ZINC000330419496 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330419496 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 646) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330419496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419496 none CNC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 647) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330419496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330419496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330419496 none CNC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.pl3', 'C.3', 'C.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, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 12, 29, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 10, 10, 10, 10, 10, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330419496 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330419496 Building ZINC000330432681 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330432681 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/648 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330432681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432681 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/649 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330432681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432681 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 34, 13, 30, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 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]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330432681 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 Building ZINC000330432681 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330432681 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 648) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330432681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432681 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 649) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330432681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432681 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 34, 13, 30, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 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]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330432681 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432681 Building ZINC000330432682 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330432682 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/650 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330432682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432682 none CN(C)C(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 34, 14, 31, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/651 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330432682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432682 none CN(C)C(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330432682 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 Building ZINC000330432682 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330432682 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 650) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330432682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432682 none CN(C)C(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 34, 14, 31, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 651) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330432682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330432682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330432682 none CN(C)C(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9] 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]) total number of confs: 89 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330432682 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330432682 Building ZINC000330467893 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330467893 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/652 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/653 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 19, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/654 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/654' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/655 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/655' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330467893 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 Building ZINC000330467893 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330467893 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 652) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 653) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 19, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 654) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 655) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330467893 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 Building ZINC000330467893 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330467893 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 652) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 653) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 19, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 654) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 655) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330467893 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 Building ZINC000330467893 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330467893 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 652) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 653) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1) `ZINC000330467893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 8, 19, 19, 19, 19, 19, 19, 5, 5, 13, 13, 13, 13, 13, 5, 2, 7, 7, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 654) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 655) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1) `ZINC000330467893.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330467893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330467893 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC[N@]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 9, 23, 23, 23, 23, 23, 21, 5, 5, 14, 14, 14, 14, 14, 5, 2, 8, 8, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330467893 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330467893 Building ZINC000330470301 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470301 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/656 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1) `ZINC000330470301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470301 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 7, 7, 28, 28, 28, 28, 28, 7, 4, 15, 15, 15, 15, 15, 15, 15, 7] 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/657 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1) `ZINC000330470301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470301 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 8, 8, 8, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 27, 27, 27, 27, 27, 8, 4, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470301 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 Building ZINC000330470301 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470301 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 656) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1) `ZINC000330470301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470301 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 7, 7, 28, 28, 28, 28, 28, 7, 4, 15, 15, 15, 15, 15, 15, 15, 7] 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 657) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1) `ZINC000330470301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470301 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 8, 8, 8, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 27, 27, 27, 27, 27, 8, 4, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470301 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470301 Building ZINC000330470303 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470303 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/658 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1) `ZINC000330470303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470303 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 9, 9, 27, 27, 27, 27, 27, 9, 4, 14, 14, 14, 14, 14, 14, 14, 9] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/659 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1) `ZINC000330470303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470303 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 7, 7, 7, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 28, 28, 28, 28, 28, 7, 4, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470303 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 Building ZINC000330470303 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470303 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 658) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1) `ZINC000330470303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470303 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 9, 9, 27, 27, 27, 27, 27, 9, 4, 14, 14, 14, 14, 14, 14, 14, 9] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 659) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1) `ZINC000330470303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330470303 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 7, 7, 7, 1, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 28, 28, 28, 28, 28, 7, 4, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470303 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470303 Building ZINC000330470658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/660 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCOCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330470658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000330470658 none CN(CCN1CCOCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 11, 30, 30, 30, 30, 30, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/661 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCOCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330470658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000330470658 none CN(CCN1CCOCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 11, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 Building ZINC000330470658 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330470658 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 660) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCOCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330470658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330470658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000330470658 none CN(CCN1CCOCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 11, 30, 30, 30, 30, 30, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 661) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCOCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330470658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330470658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000330470658 none CN(CCN1CCOCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 11, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330470658 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330470658 Building ZINC000330472280 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330472280 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/662 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1) `ZINC000330472280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330472280 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 10, 19, 19, 4, 4, 2, 2, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 10, 10, 19, 57, 4, 4, 4, 4, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/663 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1) `ZINC000330472280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330472280 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 10, 17, 17, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 10, 10, 17, 51, 6, 6, 6, 6, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472280 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 Building ZINC000330472280 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330472280 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 662) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1) `ZINC000330472280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330472280 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 10, 19, 19, 4, 4, 2, 2, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 10, 10, 19, 57, 4, 4, 4, 4, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 663) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1) `ZINC000330472280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330472280 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CC(=N)O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 10, 17, 17, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 10, 10, 17, 51, 6, 6, 6, 6, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472280 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472280 Building ZINC000330472763 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472763 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/664 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/665 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/666 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/666' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/667 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/667' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472763 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 Building ZINC000330472763 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472763 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 664) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 665) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 666) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 667) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472763 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 Building ZINC000330472763 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472763 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 664) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 665) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 666) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 667) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472763 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 Building ZINC000330472763 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472763 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 664) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 665) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 666) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 13, 16, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 667) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1) `ZINC000330472763.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472763 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472763 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472763 Building ZINC000330472764 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472764 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/668 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/669 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/670 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/670' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/671 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/671' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472764 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 Building ZINC000330472764 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472764 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 668) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 669) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 670) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 671) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472764 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 Building ZINC000330472764 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472764 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 668) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 669) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 670) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 671) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472764 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 Building ZINC000330472764 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330472764 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 668) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 669) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 670) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 671) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1) `ZINC000330472764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330472764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000330472764 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 15, 18, 18, 18, 18, 18, 18, 18, 5, 5, 12, 12, 12, 12, 12, 5, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472764 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472764 Building ZINC000330472789 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330472789 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/672 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1) `ZINC000330472789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330472789 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/673 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1) `ZINC000330472789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330472789 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 7, 12, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472789 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 Building ZINC000330472789 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330472789 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 672) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1) `ZINC000330472789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330472789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330472789 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 673) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1) `ZINC000330472789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330472789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330472789 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 7, 12, 15, 15, 15, 15, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330472789 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330472789 Building ZINC000330476503 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330476503 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/674 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330476503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476503 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/675 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330476503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476503 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [18, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330476503 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 Building ZINC000330476503 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330476503 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 674) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330476503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476503 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 675) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330476503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476503 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [18, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330476503 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476503 Building ZINC000330476505 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330476505 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/676 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330476505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476505 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/677 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330476505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476505 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330476505 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 Building ZINC000330476505 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330476505 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 676) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330476505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476505 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 677) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1) `ZINC000330476505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330476505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330476505 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330476505 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330476505 Building ZINC000330477564 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330477564 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/678 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1) `ZINC000330477564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330477564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477564 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 15, 15, 15, 6, 2, 2, 4, 4, 4, 4, 4, 2, 6, 6, 6, 6, 15, 15, 15, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/679 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1) `ZINC000330477564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330477564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477564 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 14, 14, 14, 5, 4, 4, 12, 12, 12, 12, 12, 4, 5, 5, 5, 5, 14, 14, 14, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330477564 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 Building ZINC000330477564 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330477564 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 678) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1) `ZINC000330477564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330477564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477564 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 15, 15, 15, 6, 2, 2, 4, 4, 4, 4, 4, 2, 6, 6, 6, 6, 15, 15, 15, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 679) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1) `ZINC000330477564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330477564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477564 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 14, 14, 14, 5, 4, 4, 12, 12, 12, 12, 12, 4, 5, 5, 5, 5, 14, 14, 14, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330477564 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477564 Building ZINC000330477565 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330477565 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/680 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1) `ZINC000330477565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330477565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477565 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 11, 11, 11, 11, 11, 4, 7, 7, 7, 7, 15, 15, 15, 7, 7, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/681 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1) `ZINC000330477565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330477565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477565 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 15, 15, 15, 7, 2, 2, 5, 5, 5, 5, 5, 2, 7, 7, 7, 7, 15, 15, 15, 7, 7, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330477565 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 Building ZINC000330477565 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330477565 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 680) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1) `ZINC000330477565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330477565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477565 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 11, 11, 11, 11, 11, 4, 7, 7, 7, 7, 15, 15, 15, 7, 7, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 681) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1) `ZINC000330477565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330477565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330477565 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 15, 15, 15, 7, 2, 2, 5, 5, 5, 5, 5, 2, 7, 7, 7, 7, 15, 15, 15, 7, 7, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330477565 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330477565 Building ZINC000330478803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330478803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/682 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1) `ZINC000330478803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330478803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478803 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 8, 8, 26, 26, 26, 26, 26, 8, 3, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/683 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1) `ZINC000330478803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330478803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478803 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 7, 16, 16, 16, 16, 16, 16, 16, 7, 7, 24, 24, 24, 24, 24, 7, 3, 16, 16, 16, 16, 16, 16, 16, 7] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330478803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 Building ZINC000330478803 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330478803 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 682) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1) `ZINC000330478803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330478803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478803 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 8, 8, 26, 26, 26, 26, 26, 8, 3, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 683) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1) `ZINC000330478803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330478803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478803 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 7, 16, 16, 16, 16, 16, 16, 16, 7, 7, 24, 24, 24, 24, 24, 7, 3, 16, 16, 16, 16, 16, 16, 16, 7] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330478803 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478803 Building ZINC000330478805 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330478805 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/684 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1) `ZINC000330478805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330478805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478805 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 8, 8, 26, 26, 26, 26, 26, 8, 3, 16, 16, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/685 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1) `ZINC000330478805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330478805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478805 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 8, 8, 26, 26, 26, 26, 26, 8, 3, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330478805 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 Building ZINC000330478805 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330478805 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 684) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1) `ZINC000330478805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330478805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478805 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 8, 8, 26, 26, 26, 26, 26, 8, 3, 16, 16, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 685) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1) `ZINC000330478805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330478805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330478805 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCNC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 8, 8, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 8, 8, 26, 26, 26, 26, 26, 8, 3, 14, 14, 14, 14, 14, 14, 14, 8] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330478805 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330478805 Building ZINC000330480238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330480238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/686 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/686' -> `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@H](C)C(=O)N(C)C) `ZINC000330480238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330480238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480238 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/687 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/687' -> `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@H](C)C(=O)N(C)C) `ZINC000330480238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330480238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480238 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 44, 44, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330480238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 Building ZINC000330480238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330480238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 686) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C) `ZINC000330480238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330480238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480238 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 687) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C) `ZINC000330480238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330480238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480238 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 44, 44, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330480238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480238 Building ZINC000330480251 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330480251 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/688 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/688' -> `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@@H](C)C(=O)N(C)C) `ZINC000330480251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330480251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480251 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/689 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/689' -> `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@@H](C)C(=O)N(C)C) `ZINC000330480251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330480251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480251 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330480251 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 Building ZINC000330480251 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330480251 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 688) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C) `ZINC000330480251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330480251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480251 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 689) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C) `ZINC000330480251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330480251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330480251 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N(C)C 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 43, 43, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330480251 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330480251 Building ZINC000330482626 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482626 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/690 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1) `ZINC000330482626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482626 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/691 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1) `ZINC000330482626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482626 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482626 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 Building ZINC000330482626 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482626 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 690) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1) `ZINC000330482626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482626 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 691) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1) `ZINC000330482626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482626 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482626 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482626 Building ZINC000330482627 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482627 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/692 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1) `ZINC000330482627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482627 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/693 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1) `ZINC000330482627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482627 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482627 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 Building ZINC000330482627 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482627 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 692) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1) `ZINC000330482627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482627 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 16, 16, 16, 16, 16, 16, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 693) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1) `ZINC000330482627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330482627 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2COCCO2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482627 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482627 Building ZINC000330482644 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482644 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/694 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1) `ZINC000330482644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330482644 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 16, 22, 9, 9, 6, 6, 17, 17, 17, 17, 17, 6, 9, 9, 9, 9, 16, 16, 22, 22, 66, 9, 9, 9, 9, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/695 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1) `ZINC000330482644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330482644 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 14, 17, 7, 7, 5, 5, 16, 16, 16, 16, 16, 5, 7, 7, 7, 7, 14, 14, 17, 17, 51, 7, 7, 7, 7, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482644 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 Building ZINC000330482644 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330482644 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 694) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1) `ZINC000330482644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330482644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330482644 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 16, 22, 9, 9, 6, 6, 17, 17, 17, 17, 17, 6, 9, 9, 9, 9, 16, 16, 22, 22, 66, 9, 9, 9, 9, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 695) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1) `ZINC000330482644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330482644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330482644 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 14, 17, 7, 7, 5, 5, 16, 16, 16, 16, 16, 5, 7, 7, 7, 7, 14, 14, 17, 17, 51, 7, 7, 7, 7, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330482644 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330482644 Building ZINC000330484369 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330484369 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/696 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1) `ZINC000330484369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330484369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330484369 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 5, 10, 15, 15, 15, 15, 18, 18, 15, 15, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15, 18, 18, 18, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/697 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1) `ZINC000330484369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330484369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330484369 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 2, 5, 9, 13, 13, 13, 13, 16, 16, 13, 13, 5, 5, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 16, 16, 16, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330484369 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 Building ZINC000330484369 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330484369 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 696) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1) `ZINC000330484369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330484369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330484369 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 5, 10, 15, 15, 15, 15, 18, 18, 15, 15, 5, 5, 17, 17, 17, 17, 17, 5, 15, 15, 15, 15, 18, 18, 18, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 697) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1) `ZINC000330484369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330484369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330484369 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 2, 5, 9, 13, 13, 13, 13, 16, 16, 13, 13, 5, 5, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 16, 16, 16, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330484369 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330484369 Building ZINC000330487226 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330487226 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/698 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1) `ZINC000330487226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330487226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487226 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 14, 17, 19, 19, 19, 19, 19, 6, 6, 17, 17, 17, 17, 17, 6, 3, 10, 10, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/699 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1) `ZINC000330487226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330487226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487226 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 21, 27, 27, 27, 27, 27, 5, 5, 16, 16, 16, 16, 16, 5, 2, 10, 10, 60, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330487226 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 Building ZINC000330487226 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330487226 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 698) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1) `ZINC000330487226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330487226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487226 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 14, 17, 19, 19, 19, 19, 19, 6, 6, 17, 17, 17, 17, 17, 6, 3, 10, 10, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 699) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1) `ZINC000330487226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330487226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487226 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 21, 27, 27, 27, 27, 27, 5, 5, 16, 16, 16, 16, 16, 5, 2, 10, 10, 60, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330487226 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487226 Building ZINC000330487227 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330487227 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/700 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1) `ZINC000330487227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330487227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487227 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 21, 24, 24, 24, 24, 24, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 60, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/701 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1) `ZINC000330487227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330487227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487227 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 10, 10, 57, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330487227 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 Building ZINC000330487227 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330487227 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 700) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1) `ZINC000330487227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330487227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487227 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 21, 24, 24, 24, 24, 24, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 60, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 701) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1) `ZINC000330487227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330487227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330487227 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)C2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 10, 10, 57, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330487227 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330487227 Building ZINC000330492747 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330492747 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/702 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1) `ZINC000330492747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330492747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330492747 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 17, 17, 17, 17, 17, 5, 5, 11, 11, 11, 11, 11, 5, 2, 7, 7, 20, 20, 60, 17, 17, 17, 17, 17, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/703 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1) `ZINC000330492747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330492747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330492747 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 17, 14, 14, 14, 14, 14, 5, 5, 11, 11, 11, 11, 11, 5, 2, 7, 7, 17, 17, 51, 14, 14, 14, 14, 14, 14, 14, 14, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330492747 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 Building ZINC000330492747 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330492747 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 702) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1) `ZINC000330492747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330492747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330492747 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 17, 17, 17, 17, 17, 5, 5, 11, 11, 11, 11, 11, 5, 2, 7, 7, 20, 20, 60, 17, 17, 17, 17, 17, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 703) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1) `ZINC000330492747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330492747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000330492747 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC2(CO)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 14, 17, 14, 14, 14, 14, 14, 5, 5, 11, 11, 11, 11, 11, 5, 2, 7, 7, 17, 17, 51, 14, 14, 14, 14, 14, 14, 14, 14, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330492747 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330492747 Building ZINC000330505238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330505238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/704 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/704' -> `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)NC[C@H]1COCCO1) `ZINC000330505238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330505238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505238 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 27, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/705 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/705' -> `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)NC[C@H]1COCCO1) `ZINC000330505238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330505238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505238 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 29, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330505238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 Building ZINC000330505238 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330505238 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 704) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1) `ZINC000330505238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330505238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505238 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 27, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 705) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1) `ZINC000330505238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330505238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505238 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 29, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330505238 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505238 Building ZINC000330505239 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330505239 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/706 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/706' -> `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)NC[C@@H]1COCCO1) `ZINC000330505239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330505239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505239 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 29, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/707 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/707' -> `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)NC[C@@H]1COCCO1) `ZINC000330505239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330505239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505239 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 27, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330505239 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 Building ZINC000330505239 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330505239 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 706) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1) `ZINC000330505239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330505239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505239 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 29, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 707) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1) `ZINC000330505239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330505239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330505239 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1COCCO1 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', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 27, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330505239 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330505239 Building ZINC000330512689 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512689 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/708 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512689 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 16, 16, 16, 16, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 27, 27, 27, 27, 27, 16, 16, 6, 6, 6, 6, 6, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/709 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512689 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 18, 18, 18, 4, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 28, 28, 28, 28, 28, 18, 18, 5, 5, 5, 5, 5, 18, 18, 54] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512689 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 Building ZINC000330512689 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512689 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 708) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512689 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 16, 16, 16, 16, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 27, 27, 27, 27, 27, 16, 16, 6, 6, 6, 6, 6, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 709) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512689 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 18, 18, 18, 4, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 18, 28, 28, 28, 28, 28, 18, 18, 5, 5, 5, 5, 5, 18, 18, 54] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512689 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512689 Building ZINC000330512690 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512690 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/710 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512690 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 8, 8, 8, 8, 8, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/711 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512690 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16, 10, 10, 10, 10, 10, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512690 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 Building ZINC000330512690 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512690 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 710) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512690 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 8, 8, 8, 8, 8, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 711) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512690 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16, 10, 10, 10, 10, 10, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512690 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512690 Building ZINC000330512691 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512691 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/712 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512691 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 16, 16, 16, 6, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16, 10, 10, 10, 10, 10, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/713 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512691 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 17, 17, 17, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 7, 7, 7, 7, 7, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512691 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 Building ZINC000330512691 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512691 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 712) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512691 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 16, 16, 16, 6, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16, 10, 10, 10, 10, 10, 16, 16, 48] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 713) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O) `ZINC000330512691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512691 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 17, 17, 17, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 7, 7, 7, 7, 7, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512691 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512691 Building ZINC000330512692 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512692 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/714 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512692 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 6, 6, 6, 6, 6, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 159 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/715 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512692 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 15, 15, 15, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 6, 6, 6, 6, 6, 15, 15, 45] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512692 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 Building ZINC000330512692 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330512692 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 714) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330512692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512692 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 6, 6, 6, 6, 6, 17, 17, 51] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 159 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 715) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O) `ZINC000330512692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330512692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330512692 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 15, 15, 15, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 6, 6, 6, 6, 6, 15, 15, 45] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330512692 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330512692 Building ZINC000330525798 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330525798 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/716 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/716' -> `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)NCC(=O)N(C)C) `ZINC000330525798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330525798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000330525798 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N(C)C 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/717 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/717' -> `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)NCC(=O)N(C)C) `ZINC000330525798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330525798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000330525798 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N(C)C 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330525798 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 Building ZINC000330525798 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330525798 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 716) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N(C)C) `ZINC000330525798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330525798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000330525798 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N(C)C 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 717) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N(C)C) `ZINC000330525798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330525798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000330525798 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N(C)C 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330525798 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330525798 Building ZINC000330586540 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330586540 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/718 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/718' -> `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@@H]1CCCNC1=O) `ZINC000330586540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330586540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586540 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 17, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34, 34, 34, 34] 40 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/719 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/719' -> `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@@H]1CCCNC1=O) `ZINC000330586540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330586540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586540 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 22, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330586540 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 Building ZINC000330586540 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330586540 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 718) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O) `ZINC000330586540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330586540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586540 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 17, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34, 34, 34, 34] 40 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 719) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O) `ZINC000330586540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330586540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586540 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 22, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330586540 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586540 Building ZINC000330586541 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330586541 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/720 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/720' -> `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@H]1CCCNC1=O) `ZINC000330586541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330586541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586541 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/721 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/721' -> `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@H]1CCCNC1=O) `ZINC000330586541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330586541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586541 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 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, 5, 5, 1, 1, 1, 1, 9, 9, 15, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 31, 31, 31, 31, 31, 31, 31] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330586541 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 Building ZINC000330586541 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330586541 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 720) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O) `ZINC000330586541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330586541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586541 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 721) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O) `ZINC000330586541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330586541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330586541 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 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, 5, 5, 1, 1, 1, 1, 9, 9, 15, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 31, 31, 31, 31, 31, 31, 31] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330586541 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330586541 Building ZINC000330592856 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330592856 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/722 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1) `ZINC000330592856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330592856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000330592856 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 7, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5] 23 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]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/723 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1) `ZINC000330592856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330592856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000330592856 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 22 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]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330592856 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 Building ZINC000330592856 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330592856 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 722) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1) `ZINC000330592856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330592856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000330592856 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 7, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5] 23 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]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 723) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1) `ZINC000330592856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330592856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC000330592856 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 22 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]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330592856 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330592856 Building ZINC000330594012 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330594012 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/724 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)cn1) `ZINC000330594012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330594012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594012 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 26, 28, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 26, 26, 28, 28, 84, 6] 150 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]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/725 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)cn1) `ZINC000330594012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330594012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594012 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 21, 26, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 21, 21, 26, 26, 78, 6] 150 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]) total number of confs: 189 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330594012 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 Building ZINC000330594012 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330594012 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 724) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)cn1) `ZINC000330594012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330594012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594012 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 26, 28, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 26, 26, 28, 28, 84, 6] 150 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]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 725) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)cn1) `ZINC000330594012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330594012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594012 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 21, 26, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 21, 21, 26, 26, 78, 6] 150 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]) total number of confs: 189 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330594012 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594012 Building ZINC000330594013 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330594013 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/726 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)cn1) `ZINC000330594013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330594013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594013 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 24, 27, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 24, 24, 27, 27, 81, 6] 150 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]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/727 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)cn1) `ZINC000330594013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330594013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594013 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 24, 29, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 24, 24, 29, 29, 87, 9] 150 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]) total number of confs: 207 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330594013 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 Building ZINC000330594013 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330594013 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 726) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)cn1) `ZINC000330594013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330594013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594013 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 24, 27, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 24, 24, 27, 27, 81, 6] 150 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]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 727) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)cn1) `ZINC000330594013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330594013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330594013 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2CCO)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.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 24, 29, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 24, 24, 29, 29, 87, 9] 150 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]) total number of confs: 207 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330594013 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330594013 Building ZINC000330624899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/728 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/729 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/730 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/730' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/731 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/731' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 Building ZINC000330624899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 728) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 729) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 730) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 731) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 Building ZINC000330624899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 728) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 729) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 730) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 731) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 Building ZINC000330624899 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624899 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 728) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 729) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 730) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 731) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624899.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624899 none C[C@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624899 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624899 Building ZINC000330624900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/732 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/733 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/734 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/734' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/735 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/735' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 Building ZINC000330624900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 732) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 733) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 734) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 735) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 Building ZINC000330624900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 732) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 733) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 734) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 735) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 Building ZINC000330624900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330624900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 732) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 733) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 11, 11, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 734) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 735) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330624900.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330624900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000330624900 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330624900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330624900 Building ZINC000330673089 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330673089 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/736 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1) `ZINC000330673089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330673089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330673089 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 22, 22, 22, 22, 22, 4, 4, 10, 10, 10, 10, 10, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/737 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1) `ZINC000330673089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330673089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330673089 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 20, 20, 20, 20, 20, 5, 5, 11, 11, 11, 11, 11, 5, 2, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330673089 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 Building ZINC000330673089 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330673089 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 736) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1) `ZINC000330673089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330673089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330673089 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 22, 22, 22, 22, 22, 4, 4, 10, 10, 10, 10, 10, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 737) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1) `ZINC000330673089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330673089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330673089 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 20, 20, 20, 20, 20, 5, 5, 11, 11, 11, 11, 11, 5, 2, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330673089 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330673089 Building ZINC000330685561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330685561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/738 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/739 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/740 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/740' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/741 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/741' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330685561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 Building ZINC000330685561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330685561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 738) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 739) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 740) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 741) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330685561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 Building ZINC000330685561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330685561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 738) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 739) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 740) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 741) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330685561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 Building ZINC000330685561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330685561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 738) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 739) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 740) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 741) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC2=CCN(C)CC2)cn1) `ZINC000330685561.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330685561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330685561 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2=CCN(C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 10, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330685561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330685561 Building ZINC000330709201 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709201 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/742 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/743 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/744 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/744' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/745 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/745' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709201 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 Building ZINC000330709201 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709201 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 742) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 743) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 744) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 745) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709201 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 Building ZINC000330709201 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709201 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 742) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 743) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 744) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 745) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709201 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 Building ZINC000330709201 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709201 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 742) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 743) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 744) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 745) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)cn1) `ZINC000330709201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709201 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709201 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709201 Building ZINC000330709204 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709204 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/746 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/747 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/748 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/748' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/749 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/749' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709204 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 Building ZINC000330709204 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709204 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 746) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 747) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 748) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 749) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709204 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 Building ZINC000330709204 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709204 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 746) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 747) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 748) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 749) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709204 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 Building ZINC000330709204 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330709204 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 746) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 747) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 748) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 2, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 749) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CCN(C)C2)cn1) `ZINC000330709204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330709204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330709204 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)C2)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 2, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330709204 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330709204 Building ZINC000330733295 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330733295 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/750 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/751 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/752 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/752' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/753 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/753' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330733295 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 Building ZINC000330733295 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330733295 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 750) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 751) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 752) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 753) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330733295 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 Building ZINC000330733295 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330733295 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 750) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 751) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 752) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 753) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330733295 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 Building ZINC000330733295 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000330733295 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 750) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 751) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1) `ZINC000330733295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 752) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 753) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H]2CC[N@@](C)CC2)cn1) `ZINC000330733295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000330733295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000330733295 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330733295 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330733295 Building ZINC000330745903 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330745903 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/754 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOCC2)cn1) `ZINC000330745903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330745903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330745903 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOCC2)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.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 19, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/755 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOCC2)cn1) `ZINC000330745903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330745903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330745903 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOCC2)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.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 13, 22, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 13, 13, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330745903 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 Building ZINC000330745903 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330745903 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 754) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOCC2)cn1) `ZINC000330745903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330745903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330745903 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2CCOCC2)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.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 19, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 755) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOCC2)cn1) `ZINC000330745903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330745903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000330745903 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2CCOCC2)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.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 8, 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, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 13, 22, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 2, 13, 13, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 8] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330745903 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330745903 Building ZINC000330770336 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330770336 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/756 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/756' -> `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)CC(C)(CO)CO) `ZINC000330770336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330770336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330770336 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 8, 30, 30, 40, 30, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 8, 30, 30, 30, 40, 40, 120, 40, 40, 120] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 465 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/757 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/757' -> `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)CC(C)(CO)CO) `ZINC000330770336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330770336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330770336 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 8, 29, 29, 40, 29, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 8, 29, 29, 29, 40, 40, 120, 39, 39, 117] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 468 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330770336 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 Building ZINC000330770336 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330770336 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 756) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO) `ZINC000330770336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330770336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330770336 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 8, 30, 30, 40, 30, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 8, 30, 30, 30, 40, 40, 120, 40, 40, 120] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 465 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 757) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO) `ZINC000330770336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330770336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000330770336 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(C)(CO)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 8, 29, 29, 40, 29, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 8, 29, 29, 29, 40, 40, 120, 39, 39, 117] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 468 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330770336 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330770336 Building ZINC000330809232 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330809232 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/758 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330809232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809232 none CN(C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [33, 27, 33, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 33, 33, 33, 33, 33, 33, 27, 27, 13, 13, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/759 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330809232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809232 none CN(C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [29, 22, 29, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 29, 29, 29, 29, 29, 29, 22, 22, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330809232 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 Building ZINC000330809232 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330809232 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 758) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330809232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809232 none CN(C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [33, 27, 33, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 33, 33, 33, 33, 33, 33, 27, 27, 13, 13, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 759) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330809232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809232 none CN(C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [29, 22, 29, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 29, 29, 29, 29, 29, 29, 22, 22, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330809232 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809232 Building ZINC000330809234 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330809234 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/760 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330809234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809234 none CN(C)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 30, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 30, 30, 30, 30, 30, 30, 27, 27, 11, 11, 5, 5, 5, 5, 5, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/761 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330809234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809234 none CN(C)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 31, 31, 31, 31, 31, 31, 28, 28, 11, 11, 4, 4, 4, 4, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330809234 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 Building ZINC000330809234 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330809234 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 760) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330809234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809234 none CN(C)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 30, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 30, 30, 30, 30, 30, 30, 27, 27, 11, 11, 5, 5, 5, 5, 5, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 761) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330809234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330809234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000330809234 none CN(C)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 31, 31, 31, 31, 31, 31, 28, 28, 11, 11, 4, 4, 4, 4, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330809234 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330809234 Building ZINC000330834934 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330834934 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/762 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1) `ZINC000330834934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330834934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330834934 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 6, 6, 19, 19, 19, 19, 19, 6, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/763 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1) `ZINC000330834934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330834934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330834934 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 6, 6, 19, 19, 19, 19, 19, 6, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330834934 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 Building ZINC000330834934 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330834934 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 762) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1) `ZINC000330834934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330834934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330834934 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 6, 6, 19, 19, 19, 19, 19, 6, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 763) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1) `ZINC000330834934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330834934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330834934 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 6, 6, 19, 19, 19, 19, 19, 6, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330834934 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330834934 Building ZINC000330875330 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875330 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/764 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/764' -> `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@@H]1CCN(C)C1=O) `ZINC000330875330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875330 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 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, 5, 5, 1, 1, 1, 1, 9, 9, 14, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 33, 33, 33, 33, 33, 33, 33] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/765 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/765' -> `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@@H]1CCN(C)C1=O) `ZINC000330875330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875330 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 17, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875330 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 Building ZINC000330875330 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875330 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 764) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O) `ZINC000330875330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875330 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 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, 5, 5, 1, 1, 1, 1, 9, 9, 14, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 33, 33, 33, 33, 33, 33, 33] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 765) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O) `ZINC000330875330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875330 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 17, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875330 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875330 Building ZINC000330875331 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875331 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/766 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/766' -> `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@H]1CCN(C)C1=O) `ZINC000330875331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875331 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/767 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/767' -> `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@H]1CCN(C)C1=O) `ZINC000330875331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875331 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875331 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 Building ZINC000330875331 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875331 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 766) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O) `ZINC000330875331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875331 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 767) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O) `ZINC000330875331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000330875331 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 1, 11, 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, 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] 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875331 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875331 Building ZINC000330875591 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875591 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/768 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330875591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875591 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 3, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/769 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330875591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875591 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 7, 7, 20, 20, 20, 20, 20, 7, 4, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875591 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 Building ZINC000330875591 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875591 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 768) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330875591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875591 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 6, 3, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 769) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330875591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875591 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 7, 7, 20, 20, 20, 20, 20, 7, 4, 13, 13, 13, 13, 13, 7] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875591 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875591 Building ZINC000330875592 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875592 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/770 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330875592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875592 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 7, 7, 20, 20, 20, 20, 20, 7, 4, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/771 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330875592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875592 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 6, 3, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875592 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 Building ZINC000330875592 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330875592 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 770) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330875592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330875592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875592 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 7, 7, 20, 20, 20, 20, 20, 7, 4, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 771) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330875592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330875592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000330875592 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 6, 3, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330875592 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330875592 Building ZINC000330881216 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330881216 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/772 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CO)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000330881216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330881216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000330881216 none CN(C[C@H](O)CO)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 9, 14, 14, 14, 20, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 9, 9, 42, 20, 20, 60, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 450 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 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: 212 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/773 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CO)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000330881216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330881216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000330881216 none CN(C[C@H](O)CO)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 10, 13, 13, 13, 19, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 5, 5, 5, 10, 10, 39, 19, 19, 57, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 450 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 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: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330881216 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 Building ZINC000330881216 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330881216 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 772) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CO)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000330881216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330881216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000330881216 none CN(C[C@H](O)CO)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 9, 14, 14, 14, 20, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 9, 9, 42, 20, 20, 60, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 450 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 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: 212 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 773) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CO)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000330881216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330881216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000330881216 none CN(C[C@H](O)CO)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 10, 13, 13, 13, 19, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 5, 5, 5, 10, 10, 39, 19, 19, 57, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 450 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 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: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330881216 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330881216 Building ZINC000330884345 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330884345 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/774 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/774' -> `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@H]1CNC(=O)C1) `ZINC000330884345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330884345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884345 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/775 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/775' -> `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@H]1CNC(=O)C1) `ZINC000330884345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330884345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884345 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330884345 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 Building ZINC000330884345 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330884345 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 774) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1) `ZINC000330884345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330884345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884345 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 775) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1) `ZINC000330884345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330884345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884345 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330884345 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884345 Building ZINC000330884355 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330884355 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/776 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/776' -> `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@@H]1CNC(=O)C1) `ZINC000330884355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330884355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884355 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/777 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/777' -> `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@@H]1CNC(=O)C1) `ZINC000330884355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330884355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884355 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330884355 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 Building ZINC000330884355 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330884355 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 776) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1) `ZINC000330884355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330884355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884355 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 777) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1) `ZINC000330884355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330884355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330884355 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 7, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330884355 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330884355 Building ZINC000330891597 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330891597 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/778 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330891597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891597 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 26, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 35, 35, 35, 26, 26, 12, 12, 5, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/779 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330891597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891597 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 28, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 35, 35, 35, 28, 28, 10, 10, 6, 6, 6, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330891597 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 Building ZINC000330891597 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330891597 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 778) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330891597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891597 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 26, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 35, 35, 35, 26, 26, 12, 12, 5, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 779) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330891597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891597 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 28, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 35, 35, 35, 28, 28, 10, 10, 6, 6, 6, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330891597 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891597 Building ZINC000330891598 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330891598 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/780 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330891598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891598 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 29, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 35, 35, 35, 29, 29, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/781 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330891598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891598 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 25, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 35, 35, 35, 25, 25, 10, 10, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330891598 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 Building ZINC000330891598 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330891598 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 780) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330891598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891598 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 29, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 35, 35, 35, 29, 29, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 781) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000330891598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330891598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000330891598 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 25, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 35, 35, 35, 25, 25, 10, 10, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330891598 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330891598 Building ZINC000330893314 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330893314 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/782 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/782' -> `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]2CNC(=O)C2)cn1) `ZINC000330893314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330893314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893314 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/783 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/783' -> `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]2CNC(=O)C2)cn1) `ZINC000330893314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330893314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893314 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 3, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330893314 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 Building ZINC000330893314 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330893314 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 782) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330893314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330893314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893314 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 783) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1) `ZINC000330893314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330893314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893314 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 3, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330893314 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893314 Building ZINC000330893315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330893315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/784 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/784' -> `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]2CNC(=O)C2)cn1) `ZINC000330893315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330893315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893315 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 3, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/785 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/785' -> `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]2CNC(=O)C2)cn1) `ZINC000330893315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330893315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893315 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 8, 16, 16, 8, 8, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 3, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330893315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 Building ZINC000330893315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330893315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 784) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330893315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330893315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893315 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 3, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 785) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1) `ZINC000330893315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330893315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000330893315 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CNC(=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 8, 16, 16, 8, 8, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 3, 15, 15, 15, 15, 15, 8] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330893315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330893315 Building ZINC000330959257 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959257 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/786 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959257 none C[C@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 84, 19, 19, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/787 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959257 none C[C@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 26, 26, 10, 10, 10, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 78, 19, 19, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959257 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 Building ZINC000330959257 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959257 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 786) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959257 none C[C@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 28, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 84, 19, 19, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 787) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959257 none C[C@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 26, 26, 10, 10, 10, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 78, 19, 19, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959257 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959257 Building ZINC000330959258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/788 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959258 none C[C@@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 26, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 78, 19, 19, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/789 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959258 none C[C@@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 84, 20, 20, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 Building ZINC000330959258 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959258 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 788) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959258 none C[C@@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 26, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 78, 19, 19, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 789) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959258 none C[C@@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 28, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 84, 20, 20, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959258 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959258 Building ZINC000330959259 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959259 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/790 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959259 none C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 27, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 81, 25, 25, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/791 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959259 none C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 29, 29, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 87, 23, 23, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959259 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 Building ZINC000330959259 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959259 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 790) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959259 none C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 27, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 81, 25, 25, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 791) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959259 none C[C@@H](O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 29, 29, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 87, 23, 23, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959259 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959259 Building ZINC000330959260 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959260 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/792 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959260 none C[C@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 30, 30, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 90, 23, 23, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/793 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959260 none C[C@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 27, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 81, 25, 25, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959260 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 Building ZINC000330959260 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330959260 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 792) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330959260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959260 none C[C@H](O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 30, 30, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 90, 23, 23, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 793) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330959260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330959260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330959260 none C[C@H](O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 27, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 81, 25, 25, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330959260 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330959260 Building ZINC000330961166 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330961166 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/794 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330961166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961166 none COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/795 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330961166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961166 none COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330961166 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 Building ZINC000330961166 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330961166 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 794) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330961166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961166 none COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 795) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330961166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961166 none COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330961166 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961166 Building ZINC000330961168 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330961168 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/796 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330961168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961168 none COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/797 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330961168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961168 none COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330961168 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 Building ZINC000330961168 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330961168 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 796) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330961168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961168 none COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 797) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000330961168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330961168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000330961168 none COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330961168 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330961168 Building ZINC000330998736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/798 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1) `ZINC000330998736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998736 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 12, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 21, 7, 7, 7, 7, 7, 4, 4, 16, 16, 16, 16, 16, 4, 7, 7, 21, 21, 63, 7, 7, 7, 7, 7, 4] 150 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/799 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1) `ZINC000330998736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998736 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 12, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 20, 11, 11, 11, 11, 11, 3, 3, 13, 13, 13, 13, 13, 3, 11, 11, 20, 20, 60, 11, 11, 11, 11, 11, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 Building ZINC000330998736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 798) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1) `ZINC000330998736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998736 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 12, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 21, 7, 7, 7, 7, 7, 4, 4, 16, 16, 16, 16, 16, 4, 7, 7, 21, 21, 63, 7, 7, 7, 7, 7, 4] 150 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 799) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1) `ZINC000330998736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998736 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](CO)O[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 12, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 20, 11, 11, 11, 11, 11, 3, 3, 13, 13, 13, 13, 13, 3, 11, 11, 20, 20, 60, 11, 11, 11, 11, 11, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998736 Building ZINC000330998738 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998738 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/800 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1) `ZINC000330998738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998738 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 3, 3, 13, 13, 13, 13, 13, 3, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/801 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1) `ZINC000330998738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998738 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 16, 7, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 7, 7, 7, 16, 16, 48, 7, 7, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998738 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 Building ZINC000330998738 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998738 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 800) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1) `ZINC000330998738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998738 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 3, 3, 13, 13, 13, 13, 13, 3, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 801) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1) `ZINC000330998738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998738 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 16, 7, 6, 6, 19, 19, 19, 19, 19, 6, 7, 7, 7, 7, 7, 16, 16, 48, 7, 7, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998738 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998738 Building ZINC000330998739 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998739 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/802 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1) `ZINC000330998739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998739 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 19, 7, 6, 6, 20, 20, 20, 20, 20, 6, 7, 7, 7, 7, 7, 19, 19, 57, 7, 7, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/803 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1) `ZINC000330998739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998739 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 21, 5, 6, 6, 25, 25, 25, 25, 25, 6, 5, 5, 5, 5, 5, 21, 21, 63, 5, 5, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998739 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 Building ZINC000330998739 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998739 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 802) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1) `ZINC000330998739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998739 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 19, 7, 6, 6, 20, 20, 20, 20, 20, 6, 7, 7, 7, 7, 7, 19, 19, 57, 7, 7, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 803) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1) `ZINC000330998739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998739 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 21, 5, 6, 6, 25, 25, 25, 25, 25, 6, 5, 5, 5, 5, 5, 21, 21, 63, 5, 5, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998739 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998739 Building ZINC000330998740 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998740 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/804 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1) `ZINC000330998740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998740 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 17, 5, 6, 6, 24, 24, 24, 24, 24, 6, 5, 5, 5, 5, 5, 17, 17, 51, 5, 5, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/805 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1) `ZINC000330998740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998740 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 18, 6, 6, 6, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 18, 18, 54, 6, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998740 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 Building ZINC000330998740 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330998740 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 804) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1) `ZINC000330998740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330998740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998740 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 17, 5, 6, 6, 24, 24, 24, 24, 24, 6, 5, 5, 5, 5, 5, 17, 17, 51, 5, 5, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 805) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1) `ZINC000330998740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330998740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000330998740 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@H](CO)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 18, 6, 6, 6, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 18, 18, 54, 6, 6, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000330998740 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000330998740 Building ZINC000331029146 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331029146 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/806 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000331029146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331029146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029146 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 14, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 4, 12, 12, 81, 27, 27, 27, 27, 27, 27, 7] 150 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]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/807 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000331029146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331029146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029146 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 20, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 4, 19, 19, 87, 29, 29, 29, 29, 29, 29, 10] 150 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331029146 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 Building ZINC000331029146 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331029146 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 806) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000331029146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331029146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029146 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 14, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 4, 12, 12, 81, 27, 27, 27, 27, 27, 27, 7] 150 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]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 807) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)cn1) `ZINC000331029146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331029146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029146 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 20, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 4, 19, 19, 87, 29, 29, 29, 29, 29, 29, 10] 150 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331029146 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029146 Building ZINC000331029147 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331029147 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/808 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)cn1) `ZINC000331029147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331029147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029147 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 20, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 4, 19, 19, 87, 29, 29, 29, 29, 29, 29, 10] 150 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/809 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)cn1) `ZINC000331029147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331029147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029147 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 4, 17, 17, 96, 32, 32, 32, 32, 32, 32, 11] 150 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]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331029147 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 Building ZINC000331029147 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331029147 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 808) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)cn1) `ZINC000331029147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331029147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029147 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 20, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 4, 19, 19, 87, 29, 29, 29, 29, 29, 29, 10] 150 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 809) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)cn1) `ZINC000331029147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331029147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000331029147 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCSC2)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.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 4, 17, 17, 96, 32, 32, 32, 32, 32, 32, 11] 150 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]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331029147 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331029147 Building ZINC000331064136 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331064136 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/810 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/810' -> `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)NC[C@@H](O)C(F)F) `ZINC000331064136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331064136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064136 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 39, 39, 35, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 117, 47] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/811 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/811' -> `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)NC[C@@H](O)C(F)F) `ZINC000331064136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331064136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064136 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 40, 40, 40, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 120, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 312 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331064136 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 Building ZINC000331064136 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331064136 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 810) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F) `ZINC000331064136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331064136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064136 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 39, 39, 35, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 117, 47] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 811) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F) `ZINC000331064136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331064136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064136 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 40, 40, 40, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 120, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 312 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331064136 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064136 Building ZINC000331064137 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331064137 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/812 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/812' -> `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)NC[C@H](O)C(F)F) `ZINC000331064137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331064137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064137 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 39, 39, 37, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 117, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 320 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/813 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/813' -> `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)NC[C@H](O)C(F)F) `ZINC000331064137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331064137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064137 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 23, 44, 44, 41, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 23, 23, 132, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 340 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331064137 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 Building ZINC000331064137 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331064137 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 812) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F) `ZINC000331064137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331064137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064137 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 39, 39, 37, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 117, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 320 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 813) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F) `ZINC000331064137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331064137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331064137 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)C(F)F 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', 'O.3', 'C.3', 'F', 'F', '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, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 23, 44, 44, 41, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 23, 23, 132, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 340 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331064137 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331064137 Building ZINC000331081473 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331081473 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/814 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/814' -> `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@H]1CCCN(C)C1=O) `ZINC000331081473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331081473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081473 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 22, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/815 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/815' -> `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@H]1CCCN(C)C1=O) `ZINC000331081473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331081473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081473 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 23, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331081473 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 Building ZINC000331081473 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331081473 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 814) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000331081473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331081473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081473 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 22, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 815) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000331081473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331081473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081473 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 23, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331081473 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081473 Building ZINC000331081474 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331081474 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/816 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/816' -> `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@@H]1CCCN(C)C1=O) `ZINC000331081474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331081474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081474 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 14, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/817 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/817' -> `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@@H]1CCCN(C)C1=O) `ZINC000331081474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331081474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081474 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 15, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331081474 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 Building ZINC000331081474 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331081474 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 816) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000331081474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331081474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081474 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 14, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 817) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000331081474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331081474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331081474 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 15, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331081474 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331081474 Building ZINC000331085846 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085846 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/818 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)cn1) `ZINC000331085846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085846 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 13, 13, 33, 33, 33, 33, 99, 33, 33, 6] 150 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/819 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)cn1) `ZINC000331085846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085846 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 36, 36, 36, 36, 108, 36, 36, 6] 150 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085846 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 Building ZINC000331085846 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085846 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 818) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)cn1) `ZINC000331085846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085846 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 13, 13, 33, 33, 33, 33, 99, 33, 33, 6] 150 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 819) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)cn1) `ZINC000331085846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085846 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 36, 36, 36, 36, 108, 36, 36, 6] 150 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085846 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085846 Building ZINC000331085847 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085847 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/820 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)cn1) `ZINC000331085847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085847 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 2, 12, 12, 29, 29, 29, 29, 87, 29, 29, 6] 150 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/821 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)cn1) `ZINC000331085847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085847 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 24, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 3, 15, 15, 34, 34, 34, 34, 102, 34, 34, 7] 150 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085847 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 Building ZINC000331085847 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085847 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 820) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)cn1) `ZINC000331085847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085847 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 2, 12, 12, 29, 29, 29, 29, 87, 29, 29, 6] 150 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 821) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)cn1) `ZINC000331085847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085847 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 24, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 3, 15, 15, 34, 34, 34, 34, 102, 34, 34, 7] 150 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085847 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085847 Building ZINC000331085848 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085848 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/822 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)cn1) `ZINC000331085848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085848 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 4, 16, 16, 37, 37, 37, 37, 111, 37, 37, 6] 150 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/823 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)cn1) `ZINC000331085848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085848 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 3, 14, 14, 31, 31, 31, 31, 93, 31, 31, 6] 150 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085848 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 Building ZINC000331085848 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085848 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 822) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)cn1) `ZINC000331085848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085848 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 4, 16, 16, 37, 37, 37, 37, 111, 37, 37, 6] 150 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 823) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)cn1) `ZINC000331085848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085848 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 3, 14, 14, 31, 31, 31, 31, 93, 31, 31, 6] 150 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085848 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085848 Building ZINC000331085849 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085849 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/824 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)cn1) `ZINC000331085849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085849 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 22, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 13, 13, 35, 35, 35, 35, 105, 35, 35, 5] 150 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/825 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)cn1) `ZINC000331085849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085849 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 36, 36, 36, 36, 108, 36, 36, 6] 150 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085849 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 Building ZINC000331085849 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331085849 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 824) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)cn1) `ZINC000331085849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331085849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085849 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 22, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 13, 13, 35, 35, 35, 35, 105, 35, 35, 5] 150 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 825) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)cn1) `ZINC000331085849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331085849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331085849 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC[C@H](O)C2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 36, 36, 36, 36, 108, 36, 36, 6] 150 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331085849 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331085849 Building ZINC000331086841 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331086841 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/826 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331086841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086841 none CC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 30, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 22, 22, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/827 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331086841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086841 none CC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 21, 31, 11, 11, 11, 11, 11, 11, 11, 9, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 21, 21, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331086841 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 Building ZINC000331086841 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331086841 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 826) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331086841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086841 none CC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 30, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 22, 22, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 827) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331086841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086841 none CC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 21, 31, 11, 11, 11, 11, 11, 11, 11, 9, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 21, 21, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331086841 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086841 Building ZINC000331086842 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331086842 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/828 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331086842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086842 none CC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 21, 31, 11, 11, 11, 11, 11, 11, 11, 9, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 21, 21, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/829 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331086842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086842 none CC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 31, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 31, 31, 31, 22, 22, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331086842 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 Building ZINC000331086842 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331086842 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 828) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331086842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086842 none CC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 21, 31, 11, 11, 11, 11, 11, 11, 11, 9, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 21, 21, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 829) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331086842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331086842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000331086842 none CC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens 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, 31, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 31, 31, 31, 22, 22, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331086842 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331086842 Building ZINC000331102773 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331102773 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/830 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)cn1) `ZINC000331102773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331102773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102773 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/831 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)cn1) `ZINC000331102773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331102773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102773 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 4, 4, 8, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331102773 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 Building ZINC000331102773 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331102773 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 830) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)cn1) `ZINC000331102773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331102773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102773 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 831) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)cn1) `ZINC000331102773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331102773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102773 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 4, 4, 8, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331102773 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102773 Building ZINC000331102774 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331102774 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/832 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)cn1) `ZINC000331102774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331102774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102774 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 12, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/833 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)cn1) `ZINC000331102774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331102774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102774 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 13, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331102774 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 Building ZINC000331102774 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331102774 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 832) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)cn1) `ZINC000331102774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331102774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102774 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 12, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 833) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)cn1) `ZINC000331102774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331102774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331102774 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(C)C2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 13, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331102774 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331102774 Building ZINC000331104315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331104315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/834 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331104315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104315 none COC(=O)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 32, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 32, 32, 32, 18, 18, 5, 5, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/835 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331104315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104315 none COC(=O)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 40, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 40, 40, 40, 19, 19, 6, 6, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331104315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 Building ZINC000331104315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331104315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 834) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331104315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104315 none COC(=O)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 32, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 32, 32, 32, 18, 18, 5, 5, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 835) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331104315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104315 none COC(=O)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 40, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 40, 40, 40, 19, 19, 6, 6, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331104315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104315 Building ZINC000331104316 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331104316 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/836 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331104316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104316 none COC(=O)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 40, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 40, 40, 40, 20, 20, 7, 7, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/837 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331104316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104316 none COC(=O)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 33, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 33, 33, 33, 18, 18, 4, 4, 5, 5, 5, 5, 5, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331104316 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 Building ZINC000331104316 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331104316 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 836) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331104316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104316 none COC(=O)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 40, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 40, 40, 40, 20, 20, 7, 7, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 837) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC000331104316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331104316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331104316 none COC(=O)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 33, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 33, 33, 33, 18, 18, 4, 4, 5, 5, 5, 5, 5, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331104316 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331104316 Building ZINC000331200647 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331200647 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/838 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000331200647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331200647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000331200647 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 29, 29, 11, 11, 11, 11, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 29, 29, 29, 87, 17, 17, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11, 11, 11] 150 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]) total number of confs: 216 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/839 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000331200647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331200647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000331200647 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 14, 14, 14, 14, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 30, 30, 30, 90, 19, 19, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14, 14, 14] 150 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]) total number of confs: 211 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331200647 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 Building ZINC000331200647 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331200647 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 838) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000331200647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331200647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000331200647 none C[C@H](O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 29, 29, 11, 11, 11, 11, 6, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 29, 29, 29, 87, 17, 17, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11, 11, 11] 150 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]) total number of confs: 216 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 839) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000331200647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331200647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000331200647 none C[C@H](O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 30, 14, 14, 14, 14, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 30, 30, 30, 90, 19, 19, 14, 14, 14, 14, 4, 4, 4, 4, 4, 14, 14, 14, 14] 150 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]) total number of confs: 211 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331200647 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331200647 Building ZINC000331202460 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331202460 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/840 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)cn1) `ZINC000331202460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331202460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202460 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 20, 31, 36, 9, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 31, 31, 36, 36, 108, 9, 9, 6] 150 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]) total number of confs: 233 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/841 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)cn1) `ZINC000331202460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331202460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202460 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 22, 37, 38, 12, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 37, 37, 38, 38, 114, 12, 12, 6] 150 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331202460 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 Building ZINC000331202460 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331202460 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 840) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)cn1) `ZINC000331202460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331202460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202460 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 20, 31, 36, 9, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 31, 31, 36, 36, 108, 9, 9, 6] 150 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]) total number of confs: 233 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 841) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)cn1) `ZINC000331202460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331202460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202460 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 22, 37, 38, 12, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 37, 37, 38, 38, 114, 12, 12, 6] 150 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331202460 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202460 Building ZINC000331202461 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331202461 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/842 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)cn1) `ZINC000331202461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331202461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202461 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 25, 38, 40, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 38, 38, 40, 40, 120, 14, 14, 6] 150 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]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/843 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)cn1) `ZINC000331202461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331202461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202461 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 16, 29, 36, 7, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 29, 29, 36, 36, 108, 7, 7, 6] 150 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]) total number of confs: 249 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331202461 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 Building ZINC000331202461 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331202461 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 842) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)cn1) `ZINC000331202461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331202461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202461 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 25, 38, 40, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 38, 38, 40, 40, 120, 14, 14, 6] 150 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]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 843) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)cn1) `ZINC000331202461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331202461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331202461 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OCCO)C2)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.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 16, 29, 36, 7, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 29, 29, 36, 36, 108, 7, 7, 6] 150 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]) total number of confs: 249 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331202461 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331202461 Building ZINC000331227250 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331227250 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/844 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1) `ZINC000331227250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331227250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331227250 none CNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 25, 35, 13, 13, 13, 13, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 25, 25, 13, 13, 13, 13, 3, 3, 3, 13, 13, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/845 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1) `ZINC000331227250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331227250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331227250 none CNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 35, 13, 13, 13, 13, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 23, 23, 13, 13, 13, 13, 3, 3, 3, 13, 13, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331227250 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 Building ZINC000331227250 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331227250 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 844) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1) `ZINC000331227250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331227250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331227250 none CNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 25, 35, 13, 13, 13, 13, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 25, 25, 13, 13, 13, 13, 3, 3, 3, 13, 13, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 845) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1) `ZINC000331227250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331227250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000331227250 none CNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 35, 13, 13, 13, 13, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 23, 23, 13, 13, 13, 13, 3, 3, 3, 13, 13, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331227250 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331227250 Building ZINC000331251206 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331251206 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/846 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331251206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251206 none NS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 20, 49, 49, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 49, 49, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/847 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331251206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251206 none NS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 49, 49, 21, 21, 21, 21, 5, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 49, 49, 21, 21, 21, 21, 3, 3, 6, 3, 3, 21, 21] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331251206 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 Building ZINC000331251206 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331251206 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 846) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331251206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251206 none NS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 20, 49, 49, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 49, 49, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 847) grep: /scratch/xiaobo/121205/xcw-8058088.75/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: NS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331251206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251206 none NS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 49, 49, 21, 21, 21, 21, 5, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 49, 49, 21, 21, 21, 21, 3, 3, 6, 3, 3, 21, 21] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331251206 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251206 Building ZINC000331251207 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331251207 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/848 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331251207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251207 none NS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 19, 49, 49, 19, 19, 19, 19, 4, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 49, 49, 19, 19, 19, 19, 3, 3, 6, 3, 3, 19, 19] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/849 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331251207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251207 none NS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 20, 49, 49, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 49, 49, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331251207 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 Building ZINC000331251207 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331251207 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 848) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331251207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251207 none NS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 19, 49, 49, 19, 19, 19, 19, 4, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 49, 49, 19, 19, 19, 19, 3, 3, 6, 3, 3, 19, 19] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 849) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC000331251207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331251207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000331251207 none NS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 20, 49, 49, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 49, 49, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331251207 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331251207 Building ZINC000331268061 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268061 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/850 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268061 none COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 11, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 24, 33, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/851 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268061 none COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 15, 28, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 45, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268061 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 Building ZINC000331268061 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268061 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 850) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268061 none COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 11, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 24, 33, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 851) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268061 none COC(=O)[C@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 15, 28, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 45, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268061 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268061 Building ZINC000331268062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/852 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268062 none COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 16, 27, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 48, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/853 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268062 none COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 36, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 Building ZINC000331268062 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268062 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 852) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268062 none COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 16, 27, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 27, 27, 27, 48, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 853) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268062 none COC(=O)[C@@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 36, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268062 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268062 Building ZINC000331268063 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268063 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/854 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268063 none COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 36, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/855 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268063 none COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 14, 14, 14, 14, 14, 14, 14, 14, 7, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 42, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268063 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 Building ZINC000331268063 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268063 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 854) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268063 none COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 7, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 36, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 855) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268063 none COC(=O)[C@H]1[C@@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 14, 27, 14, 14, 14, 14, 14, 14, 14, 14, 7, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 42, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268063 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268063 Building ZINC000331268064 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268064 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/856 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268064 none COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 12, 12, 12, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 36, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/857 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268064 none COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 13, 13, 13, 13, 13, 13, 13, 13, 7, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 39, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268064 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 Building ZINC000331268064 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331268064 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 856) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331268064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268064 none COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 12, 12, 12, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 36, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 857) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331268064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331268064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000331268064 none COC(=O)[C@@H]1[C@H](O)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 13, 26, 13, 13, 13, 13, 13, 13, 13, 13, 7, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 39, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331268064 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331268064 Building ZINC000331286610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/858 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286610 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/859 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286610 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 175 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 Building ZINC000331286610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 858) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286610 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 859) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286610 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 175 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286610 Building ZINC000331286611 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286611 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/860 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286611 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 27, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 27, 27, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/861 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286611 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286611 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 Building ZINC000331286611 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286611 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 860) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286611 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 27, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 27, 27, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 861) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286611 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286611 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286611 Building ZINC000331286612 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286612 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/862 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286612 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/863 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286612 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 26, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286612 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 Building ZINC000331286612 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286612 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 862) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286612 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 863) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO) `ZINC000331286612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286612 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 26, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286612 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286612 Building ZINC000331286613 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286613 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/864 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286613 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/865 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286613 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286613 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 Building ZINC000331286613 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331286613 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 864) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331286613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286613 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 26, 26, 78] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 865) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO) `ZINC000331286613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331286613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331286613 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 29, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 29, 29, 87] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331286613 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331286613 Building ZINC000331318607 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318607 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/866 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318607 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 57, 19, 19, 19, 19, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/867 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318607 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 15, 15, 6, 6, 21, 21, 21, 21, 21, 6, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318607 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 Building ZINC000331318607 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318607 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 866) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318607 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 57, 19, 19, 19, 19, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 867) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318607 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 15, 15, 15, 15, 15, 15, 15, 6, 6, 21, 21, 21, 21, 21, 6, 3, 14, 14, 45, 15, 15, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318607 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318607 Building ZINC000331318608 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318608 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/868 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318608 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 48, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/869 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318608 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 48, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318608 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 Building ZINC000331318608 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318608 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 868) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318608 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 48, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 869) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1) `ZINC000331318608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318608 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 48, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318608 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318608 Building ZINC000331318609 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318609 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/870 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1) `ZINC000331318609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318609 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 51, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/871 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1) `ZINC000331318609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318609 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 22, 22, 22, 22, 22, 22, 22, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 66, 22, 22, 22, 22, 22, 22, 22, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318609 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 Building ZINC000331318609 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318609 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 870) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1) `ZINC000331318609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318609 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 51, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 871) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1) `ZINC000331318609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318609 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 22, 22, 22, 22, 22, 22, 22, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 66, 22, 22, 22, 22, 22, 22, 22, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318609 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318609 Building ZINC000331318610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/872 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1) `ZINC000331318610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318610 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 13, 13, 13, 13, 13, 13, 13, 6, 6, 17, 17, 17, 17, 17, 6, 2, 11, 11, 39, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/873 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1) `ZINC000331318610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318610 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 6, 6, 22, 22, 22, 22, 22, 6, 2, 13, 13, 51, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 Building ZINC000331318610 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331318610 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 872) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1) `ZINC000331318610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331318610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318610 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 13, 13, 13, 13, 13, 13, 13, 6, 6, 17, 17, 17, 17, 17, 6, 2, 11, 11, 39, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 873) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1) `ZINC000331318610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331318610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331318610 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(O)CCO[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 6, 6, 22, 22, 22, 22, 22, 6, 2, 13, 13, 51, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331318610 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331318610 Building ZINC000331337779 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331337779 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/874 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/874' -> `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@@]1(CCO)CCOC1) `ZINC000331337779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331337779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337779 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 15, 29, 46, 50, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 46, 46, 50, 50, 150, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/875 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/875' -> `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@@]1(CCO)CCOC1) `ZINC000331337779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331337779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337779 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 14, 26, 45, 46, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 45, 45, 46, 46, 138, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 310 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331337779 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 Building ZINC000331337779 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331337779 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 874) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000331337779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331337779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337779 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 15, 29, 46, 50, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 46, 46, 50, 50, 150, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 875) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000331337779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331337779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337779 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 14, 26, 45, 46, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 45, 45, 46, 46, 138, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 310 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331337779 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337779 Building ZINC000331337780 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331337780 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/876 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/876' -> `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@]1(CCO)CCOC1) `ZINC000331337780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331337780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337780 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 14, 27, 45, 46, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 45, 45, 46, 46, 138, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/877 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/877' -> `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@]1(CCO)CCOC1) `ZINC000331337780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331337780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337780 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 15, 29, 46, 50, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 46, 46, 50, 50, 150, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331337780 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 Building ZINC000331337780 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331337780 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 876) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000331337780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331337780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337780 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 14, 27, 45, 46, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 45, 45, 46, 46, 138, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 877) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000331337780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331337780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000331337780 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 15, 29, 46, 50, 29, 29, 29, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 46, 46, 50, 50, 150, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331337780 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331337780 Building ZINC000331340110 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331340110 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/878 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1) `ZINC000331340110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331340110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340110 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 9, 15, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 9, 9, 15, 15, 45, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/879 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1) `ZINC000331340110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331340110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340110 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 10, 15, 8, 8, 8, 8, 6, 6, 17, 17, 17, 17, 17, 6, 3, 10, 10, 15, 15, 45, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331340110 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 Building ZINC000331340110 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331340110 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 878) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1) `ZINC000331340110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331340110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340110 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 9, 15, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 9, 9, 15, 15, 45, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 879) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1) `ZINC000331340110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331340110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340110 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 10, 15, 8, 8, 8, 8, 6, 6, 17, 17, 17, 17, 17, 6, 3, 10, 10, 15, 15, 45, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331340110 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340110 Building ZINC000331340113 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331340113 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/880 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1) `ZINC000331340113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331340113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340113 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 9, 11, 16, 9, 9, 9, 9, 7, 7, 18, 18, 18, 18, 18, 7, 4, 11, 11, 16, 16, 48, 9, 9, 9, 9, 9, 9, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/881 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1) `ZINC000331340113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331340113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340113 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 8, 13, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 13, 13, 39, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331340113 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 Building ZINC000331340113 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331340113 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 880) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1) `ZINC000331340113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331340113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340113 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 9, 11, 16, 9, 9, 9, 9, 7, 7, 18, 18, 18, 18, 18, 7, 4, 11, 11, 16, 16, 48, 9, 9, 9, 9, 9, 9, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 881) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1) `ZINC000331340113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331340113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331340113 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCO)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 8, 13, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 13, 13, 39, 8, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331340113 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331340113 Building ZINC000331453880 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331453880 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/882 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1) `ZINC000331453880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331453880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331453880 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 8, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/883 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1) `ZINC000331453880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331453880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331453880 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 9, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331453880 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 Building ZINC000331453880 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331453880 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 882) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1) `ZINC000331453880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331453880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331453880 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 8, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 19, 19, 19, 19, 19, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 883) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1) `ZINC000331453880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331453880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331453880 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]3C(=O)NC[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 9, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331453880 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331453880 Building ZINC000331459115 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331459115 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/884 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)cn1) `ZINC000331459115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331459115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459115 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 18, 30, 30, 27, 33, 33, 8, 8, 8, 8, 8, 8, 4, 18, 18, 30, 30, 30, 90, 33, 33, 33, 33, 33, 8] 150 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]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/885 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)cn1) `ZINC000331459115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331459115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459115 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 16, 30, 30, 26, 34, 34, 8, 8, 8, 8, 8, 8, 4, 16, 16, 30, 30, 30, 90, 34, 34, 34, 34, 34, 8] 150 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]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331459115 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 Building ZINC000331459115 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331459115 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 884) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)cn1) `ZINC000331459115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331459115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459115 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 18, 30, 30, 27, 33, 33, 8, 8, 8, 8, 8, 8, 4, 18, 18, 30, 30, 30, 90, 33, 33, 33, 33, 33, 8] 150 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]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 885) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)cn1) `ZINC000331459115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331459115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459115 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 16, 30, 30, 26, 34, 34, 8, 8, 8, 8, 8, 8, 4, 16, 16, 30, 30, 30, 90, 34, 34, 34, 34, 34, 8] 150 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]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331459115 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459115 Building ZINC000331459146 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331459146 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/886 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)cn1) `ZINC000331459146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331459146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459146 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 15, 25, 26, 24, 29, 29, 7, 7, 7, 7, 7, 7, 4, 15, 15, 26, 26, 26, 78, 29, 29, 29, 29, 29, 7] 150 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]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/887 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)cn1) `ZINC000331459146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331459146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459146 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 24, 25, 22, 26, 26, 7, 7, 7, 7, 7, 7, 3, 14, 14, 25, 25, 25, 75, 26, 26, 26, 26, 26, 7] 150 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]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331459146 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 Building ZINC000331459146 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331459146 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 886) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)cn1) `ZINC000331459146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331459146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459146 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 15, 25, 26, 24, 29, 29, 7, 7, 7, 7, 7, 7, 4, 15, 15, 26, 26, 26, 78, 29, 29, 29, 29, 29, 7] 150 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]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 887) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)cn1) `ZINC000331459146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331459146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331459146 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C2CC2)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 24, 25, 22, 26, 26, 7, 7, 7, 7, 7, 7, 3, 14, 14, 25, 25, 25, 75, 26, 26, 26, 26, 26, 7] 150 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]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331459146 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331459146 Building ZINC000331474127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331474127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/888 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000331474127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331474127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000331474127 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)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.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', '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, 5, 5, 8, 8, 8, 8, 1, 1, 8, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11] 44 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]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/889 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000331474127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331474127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000331474127 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)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.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', '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, 5, 5, 8, 8, 8, 8, 1, 1, 8, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11] 44 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]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331474127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 Building ZINC000331474127 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331474127 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 888) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000331474127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331474127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000331474127 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)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.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', '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, 5, 5, 8, 8, 8, 8, 1, 1, 8, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11] 44 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]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 889) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)cn1) `ZINC000331474127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331474127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000331474127 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCCn3nnnc32)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.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', '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, 5, 5, 8, 8, 8, 8, 1, 1, 8, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11] 44 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]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331474127 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331474127 Building ZINC000331510904 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331510904 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/890 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 20, 20, 20, 20, 15, 20, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 20, 34, 34, 34, 34, 34, 20, 20, 60, 15, 15, 2, 7, 7, 7, 7, 7, 20, 20] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/891 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 25, 25, 25, 25, 20, 25, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 40, 40, 40, 40, 40, 25, 25, 75, 14, 14, 2, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/892 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/892' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 18, 18, 18, 14, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 18, 18, 54, 13, 13, 2, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/893 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/893' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 25, 25, 25, 25, 20, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 25, 37, 37, 37, 37, 37, 25, 25, 75, 14, 14, 3, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331510904 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 Building ZINC000331510904 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331510904 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 890) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 20, 20, 20, 20, 15, 20, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 20, 34, 34, 34, 34, 34, 20, 20, 60, 15, 15, 2, 7, 7, 7, 7, 7, 20, 20] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 891) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 25, 25, 25, 25, 20, 25, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 40, 40, 40, 40, 40, 25, 25, 75, 14, 14, 2, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 892) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 18, 18, 18, 14, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 18, 18, 54, 13, 13, 2, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 893) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 25, 25, 25, 25, 20, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 25, 37, 37, 37, 37, 37, 25, 25, 75, 14, 14, 3, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331510904 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 Building ZINC000331510904 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331510904 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 890) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 20, 20, 20, 20, 15, 20, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 20, 34, 34, 34, 34, 34, 20, 20, 60, 15, 15, 2, 7, 7, 7, 7, 7, 20, 20] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 891) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 25, 25, 25, 25, 20, 25, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 40, 40, 40, 40, 40, 25, 25, 75, 14, 14, 2, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 892) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 18, 18, 18, 14, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 18, 18, 54, 13, 13, 2, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 893) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 25, 25, 25, 25, 20, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 25, 37, 37, 37, 37, 37, 25, 25, 75, 14, 14, 3, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331510904 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 Building ZINC000331510904 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331510904 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 890) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 20, 20, 20, 20, 15, 20, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 20, 34, 34, 34, 34, 34, 20, 20, 60, 15, 15, 2, 7, 7, 7, 7, 7, 20, 20] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 891) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 25, 25, 25, 25, 20, 25, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 40, 40, 40, 40, 40, 25, 25, 75, 14, 14, 2, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 892) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 18, 18, 18, 14, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 18, 18, 54, 13, 13, 2, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 893) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000331510904.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331510904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000331510904 none CCO[C@H]1C[C@@](O)(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 25, 25, 25, 25, 20, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 25, 37, 37, 37, 37, 37, 25, 25, 75, 14, 14, 3, 5, 5, 5, 5, 5, 25, 25] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331510904 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331510904 Building ZINC000331572388 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331572388 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/894 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331572388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331572388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331572388 none CN(CC1(O)CCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 23, 27, 27, 27, 27, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 18, 18, 81, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/895 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331572388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331572388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331572388 none CN(CC1(O)CCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 24, 28, 28, 28, 28, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 20, 20, 84, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 187 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331572388 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 Building ZINC000331572388 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331572388 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 894) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331572388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331572388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331572388 none CN(CC1(O)CCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 23, 27, 27, 27, 27, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 18, 18, 81, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 895) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331572388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331572388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331572388 none CN(CC1(O)CCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 24, 28, 28, 28, 28, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 20, 20, 84, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 187 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331572388 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331572388 Building ZINC000331605489 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331605489 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/896 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)cn1) `ZINC000331605489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331605489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605489 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 10, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/897 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)cn1) `ZINC000331605489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331605489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605489 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331605489 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 Building ZINC000331605489 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331605489 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 896) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)cn1) `ZINC000331605489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331605489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605489 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 10, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 897) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)cn1) `ZINC000331605489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331605489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605489 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 9, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331605489 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605489 Building ZINC000331605497 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331605497 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/898 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)cn1) `ZINC000331605497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331605497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605497 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 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]) total number of confs: 61 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/899 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)cn1) `ZINC000331605497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331605497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605497 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331605497 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 Building ZINC000331605497 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331605497 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 898) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)cn1) `ZINC000331605497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331605497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605497 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12] 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]) total number of confs: 61 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 899) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)cn1) `ZINC000331605497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331605497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000331605497 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCCNC2=O)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 1, 1, 1, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331605497 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331605497 Building ZINC000331704856 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331704856 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/900 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(CO)CC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331704856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331704856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331704856 none CN(CC1(CO)CC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 14, 24, 31, 24, 24, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 31, 31, 93, 24, 24, 24, 24, 6, 6, 6, 6, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 217 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/901 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(CO)CC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331704856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331704856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331704856 none CN(CC1(CO)CC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 12, 20, 30, 20, 20, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 12, 12, 30, 30, 90, 20, 20, 20, 20, 6, 6, 6, 6, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331704856 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 Building ZINC000331704856 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331704856 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 900) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(CO)CC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331704856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331704856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331704856 none CN(CC1(CO)CC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 14, 24, 31, 24, 24, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 31, 31, 93, 24, 24, 24, 24, 6, 6, 6, 6, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 217 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 901) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(CO)CC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000331704856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331704856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331704856 none CN(CC1(CO)CC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 12, 20, 30, 20, 20, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 12, 12, 30, 30, 90, 20, 20, 20, 20, 6, 6, 6, 6, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331704856 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331704856 Building ZINC000331747588 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331747588 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/902 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/903 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/904 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/904' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/905 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/905' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331747588 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 Building ZINC000331747588 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331747588 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 902) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 903) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 904) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 905) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331747588 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 Building ZINC000331747588 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331747588 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 902) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 903) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 904) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 905) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331747588 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 Building ZINC000331747588 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331747588 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 902) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 903) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 904) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need 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, 1, 1, 4, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 905) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3OCCN(C)[C@H]3C2)cn1) `ZINC000331747588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331747588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000331747588 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3OCCN(C)[C@H]3C2)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.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331747588 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331747588 Building ZINC000331776411 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331776411 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/906 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000331776411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331776411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331776411 none CCNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 7, 16, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 28, 28, 28, 28, 28, 16, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/907 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000331776411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331776411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331776411 none CCNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 15, 6, 15, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 28, 28, 28, 28, 28, 15, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331776411 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 Building ZINC000331776411 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331776411 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 906) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000331776411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331776411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331776411 none CCNC(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 7, 16, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 28, 28, 28, 28, 28, 16, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 907) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000331776411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331776411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331776411 none CCNC(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 15, 6, 15, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 28, 28, 28, 28, 28, 15, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331776411 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331776411 Building ZINC000331911453 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331911453 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/908 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/908' -> `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)NC1(CO)CC1) `ZINC000331911453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331911453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331911453 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CO)CC1 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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 32, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 32, 32, 96, 17, 17, 17, 17] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/909 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/909' -> `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)NC1(CO)CC1) `ZINC000331911453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331911453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331911453 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CO)CC1 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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 32, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 32, 32, 96, 17, 17, 17, 17] 111 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331911453 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 Building ZINC000331911453 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331911453 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 908) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CO)CC1) `ZINC000331911453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331911453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331911453 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CO)CC1 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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 32, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 32, 32, 96, 17, 17, 17, 17] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 909) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CO)CC1) `ZINC000331911453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331911453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000331911453 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CO)CC1 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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 32, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 32, 32, 96, 17, 17, 17, 17] 111 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331911453 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331911453 Building ZINC000331928721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/910 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/911 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/912 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/912' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/913 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/913' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 Building ZINC000331928721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 910) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 911) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 912) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 913) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 Building ZINC000331928721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 910) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 911) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 912) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 913) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 Building ZINC000331928721 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928721 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 910) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 911) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 912) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 45 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 913) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928721.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928721 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 49 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928721 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928721 Building ZINC000331928727 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928727 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/914 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/915 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/916 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/916' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/917 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/917' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928727 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 Building ZINC000331928727 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928727 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 914) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 915) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 916) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 917) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928727 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 Building ZINC000331928727 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928727 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 914) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 915) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 916) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 917) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928727 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 Building ZINC000331928727 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928727 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 914) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 915) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 916) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 16, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 917) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928727.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928727 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 20, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928727 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928727 Building ZINC000331928732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/918 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/919 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/920 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/920' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/921 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/921' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 Building ZINC000331928732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 918) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 919) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 920) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 921) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 Building ZINC000331928732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 918) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 919) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 920) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 921) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 Building ZINC000331928732 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928732 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 918) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 919) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 920) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 921) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@H]3CCN(C)C[C@@H]32)cn1) `ZINC000331928732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928732 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H]3CCN(C)C[C@@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 13, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928732 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928732 Building ZINC000331928736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/922 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/923 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/924 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/924' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/925 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/925' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 Building ZINC000331928736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 922) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 923) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 924) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 925) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 Building ZINC000331928736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 922) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 923) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 924) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 925) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 Building ZINC000331928736 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000331928736 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 922) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 923) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `2' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 2 (index: 924) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 13, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `3' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 3 (index: 925) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCO[C@@H]3CCN(C)C[C@H]32)cn1) `ZINC000331928736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000331928736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000331928736 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H]3CCN(C)C[C@H]32)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.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 15, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000331928736 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/0.* 2: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/2.* 3: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/3.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000331928736 Building ZINC000332041984 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332041984 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/926 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)cn1) `ZINC000332041984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332041984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332041984 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 18, 23, 10, 22, 22, 22, 6, 6, 6, 6, 6, 6, 18, 18, 23, 23, 69, 22, 22, 22, 22, 22, 22, 22, 6] 150 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]) total number of confs: 204 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/927 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)cn1) `ZINC000332041984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332041984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332041984 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 5, 5, 10, 17, 25, 12, 23, 23, 23, 5, 5, 5, 5, 5, 5, 17, 17, 25, 25, 75, 23, 23, 23, 23, 23, 23, 23, 5] 150 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]) total number of confs: 222 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332041984 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 Building ZINC000332041984 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332041984 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 926) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)cn1) `ZINC000332041984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332041984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332041984 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 18, 23, 10, 22, 22, 22, 6, 6, 6, 6, 6, 6, 18, 18, 23, 23, 69, 22, 22, 22, 22, 22, 22, 22, 6] 150 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]) total number of confs: 204 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 927) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)cn1) `ZINC000332041984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332041984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332041984 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CCO)C2CCC2)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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 5, 5, 10, 17, 25, 12, 23, 23, 23, 5, 5, 5, 5, 5, 5, 17, 17, 25, 25, 75, 23, 23, 23, 23, 23, 23, 23, 5] 150 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]) total number of confs: 222 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332041984 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332041984 Building ZINC000332113670 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332113670 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/928 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113670 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 5, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/929 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113670 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332113670 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 Building ZINC000332113670 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332113670 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 928) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113670 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 5, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 929) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113670 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332113670 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113670 Building ZINC000332113671 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332113671 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/930 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113671 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/931 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113671 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 5, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332113671 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 Building ZINC000332113671 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332113671 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 930) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113671 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 931) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)cn1) `ZINC000332113671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332113671 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c[nH]nc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 5, 27, 27, 27, 27, 27, 27, 27, 11] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332113671 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332113671 Building ZINC000332174436 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332174436 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/932 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1) `ZINC000332174436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332174436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174436 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/933 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1) `ZINC000332174436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332174436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174436 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332174436 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 Building ZINC000332174436 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332174436 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 932) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1) `ZINC000332174436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332174436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174436 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 933) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1) `ZINC000332174436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332174436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174436 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332174436 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174436 Building ZINC000332174437 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332174437 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/934 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1) `ZINC000332174437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332174437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174437 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/935 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1) `ZINC000332174437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332174437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174437 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332174437 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 Building ZINC000332174437 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332174437 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 934) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1) `ZINC000332174437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332174437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174437 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 935) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1) `ZINC000332174437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332174437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000332174437 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3ncnn3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 6, 3, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332174437 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332174437 Building ZINC000332202898 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332202898 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/936 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332202898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202898 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/937 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332202898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202898 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332202898 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 Building ZINC000332202898 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332202898 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 936) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332202898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202898 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 937) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332202898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202898 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 26, 10] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332202898 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202898 Building ZINC000332202900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332202900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/938 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332202900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202900 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 5, 29, 29, 29, 29, 29, 29, 29, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/939 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332202900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202900 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332202900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 Building ZINC000332202900 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332202900 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 938) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332202900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202900 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 5, 29, 29, 29, 29, 29, 29, 29, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 939) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)cn1) `ZINC000332202900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332202900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000332202900 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', '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, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 11, 1, 1, 1, 1, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 5, 28, 28, 28, 28, 28, 28, 28, 11] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332202900 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332202900 Building ZINC000332264165 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332264165 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/940 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1) `ZINC000332264165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332264165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264165 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 9, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 18, 18, 18, 18, 18, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/941 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1) `ZINC000332264165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332264165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264165 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332264165 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 Building ZINC000332264165 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332264165 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 940) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1) `ZINC000332264165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332264165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264165 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 2, 9, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 18, 18, 18, 18, 18, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 941) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1) `ZINC000332264165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332264165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264165 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332264165 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264165 Building ZINC000332264167 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332264167 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/942 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1) `ZINC000332264167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332264167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264167 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 23, 23, 23, 23, 23, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/943 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1) `ZINC000332264167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332264167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264167 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 6, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 16, 16, 16, 16, 16, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332264167 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 Building ZINC000332264167 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332264167 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 942) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1) `ZINC000332264167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332264167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264167 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 2, 7, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 23, 23, 23, 23, 23, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 943) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1) `ZINC000332264167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332264167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000332264167 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN3C(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 2, 6, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 16, 16, 16, 16, 16, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332264167 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332264167 Building ZINC000332320561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332320561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/944 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1) `ZINC000332320561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332320561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000332320561 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/945 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1) `ZINC000332320561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332320561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000332320561 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 7, 7, 18, 18, 18, 18, 18, 7, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332320561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 Building ZINC000332320561 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332320561 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 944) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1) `ZINC000332320561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332320561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000332320561 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 17, 17, 17, 17, 6, 6, 16, 16, 16, 16, 16, 6, 3, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 945) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1) `ZINC000332320561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332320561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000332320561 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC(=O)N2CCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 7, 7, 18, 18, 18, 18, 18, 7, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332320561 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332320561 Building ZINC000332343441 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332343441 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/946 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/946' -> `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)NCC(=O)N1CCCC1) `ZINC000332343441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332343441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000332343441 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/947 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/947' -> `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)NCC(=O)N1CCCC1) `ZINC000332343441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332343441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000332343441 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 44, 44, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332343441 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 Building ZINC000332343441 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000332343441 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 946) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1) `ZINC000332343441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000332343441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000332343441 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 947) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1) `ZINC000332343441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000332343441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000332343441 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1 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.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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 44, 44, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000332343441 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000332343441 Building ZINC000334737315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000334737315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/948 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000334737315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000334737315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000334737315 none CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 30, 39, 30, 30, 30, 15, 1, 21, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/949 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000334737315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000334737315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000334737315 none CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 39, 32, 32, 32, 15, 1, 23, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 39, 39, 39, 39, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000334737315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 Building ZINC000334737315 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000334737315 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 948) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000334737315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000334737315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000334737315 none CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 30, 39, 30, 30, 30, 15, 1, 21, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 949) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1) `ZINC000334737315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000334737315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000334737315 none CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 39, 32, 32, 32, 15, 1, 23, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 39, 39, 39, 39, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000334737315 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000334737315 Building ZINC000335187052 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335187052 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/950 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1) `ZINC000335187052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335187052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000335187052 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 37, 37, 12, 6, 6, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 12, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/951 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1) `ZINC000335187052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335187052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000335187052 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 38, 38, 13, 5, 5, 5, 5, 5, 5, 13, 13, 38, 38, 38, 38, 38, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335187052 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 Building ZINC000335187052 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335187052 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 950) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1) `ZINC000335187052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335187052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000335187052 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 37, 37, 12, 6, 6, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 12, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 951) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1) `ZINC000335187052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335187052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000335187052 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 38, 38, 13, 5, 5, 5, 5, 5, 5, 13, 13, 38, 38, 38, 38, 38, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335187052 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335187052 Building ZINC000335321668 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335321668 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/952 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21) `ZINC000335321668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335321668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000335321668 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/953 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21) `ZINC000335321668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335321668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000335321668 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 15, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26] 41 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335321668 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 Building ZINC000335321668 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335321668 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 952) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21) `ZINC000335321668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335321668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000335321668 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 16, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 953) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21) `ZINC000335321668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335321668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000335321668 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]2C(=O)NC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 15, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26] 41 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 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: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335321668 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335321668 Building ZINC000335652189 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335652189 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/954 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335652189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652189 none CNC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 32, 42, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 46, 46, 46, 46, 32, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 137 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/955 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335652189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652189 none CNC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 34, 24, 34, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 42, 42, 42, 42, 24, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335652189 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 Building ZINC000335652189 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335652189 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 954) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335652189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652189 none CNC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 32, 42, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 46, 46, 46, 46, 32, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 137 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 955) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335652189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652189 none CNC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 34, 24, 34, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 42, 42, 42, 42, 24, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335652189 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652189 Building ZINC000335652190 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335652190 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/956 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335652190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652190 none CNC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 35, 26, 35, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 42, 42, 42, 42, 26, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 130 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/957 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335652190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652190 none CNC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 29, 40, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 44, 44, 44, 44, 29, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335652190 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 Building ZINC000335652190 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335652190 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 956) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335652190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652190 none CNC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 35, 26, 35, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 42, 42, 42, 42, 26, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 130 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 957) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1) `ZINC000335652190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335652190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000335652190 none CNC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 29, 40, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 44, 44, 44, 44, 29, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335652190 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335652190 Building ZINC000335743624 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335743624 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/958 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O) `ZINC000335743624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335743624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743624 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need 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, 1, 1, 1, 1, 8, 8, 14, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/959 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O) `ZINC000335743624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335743624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743624 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need 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, 1, 1, 1, 1, 9, 9, 16, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335743624 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 Building ZINC000335743624 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335743624 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 958) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O) `ZINC000335743624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335743624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743624 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need 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, 1, 1, 1, 1, 8, 8, 14, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 959) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O) `ZINC000335743624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335743624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743624 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need 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, 1, 1, 1, 1, 9, 9, 16, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335743624 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743624 Building ZINC000335743625 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335743625 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/960 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O) `ZINC000335743625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335743625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743625 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 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: [8, 8, 8, 8, 8, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21] 39 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 69 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/961 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O) `ZINC000335743625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335743625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743625 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31] 45 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335743625 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 Building ZINC000335743625 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335743625 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 960) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O) `ZINC000335743625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335743625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743625 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 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: [8, 8, 8, 8, 8, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21] 39 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 69 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 961) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O) `ZINC000335743625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335743625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335743625 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31] 45 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335743625 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335743625 Building ZINC000335834419 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335834419 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/962 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O) `ZINC000335834419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335834419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834419 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 7, 7, 7, 7, 7, 7, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/963 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O) `ZINC000335834419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335834419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834419 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 6, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335834419 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 Building ZINC000335834419 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335834419 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 962) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O) `ZINC000335834419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335834419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834419 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 7, 7, 7, 7, 7, 7, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 963) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O) `ZINC000335834419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335834419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834419 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 6, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335834419 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834419 Building ZINC000335834421 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335834421 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/964 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O) `ZINC000335834421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335834421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834421 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 6, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/965 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O) `ZINC000335834421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335834421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834421 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 7, 7, 7, 7, 7, 7, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335834421 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 Building ZINC000335834421 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335834421 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 964) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O) `ZINC000335834421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335834421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834421 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 6, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 965) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O) `ZINC000335834421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335834421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000335834421 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 20, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 7, 7, 7, 7, 7, 7, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335834421 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335834421 Building ZINC000335972892 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335972892 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/966 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000335972892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335972892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000335972892 none C[C@H]1C(=O)NCCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6] 26 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/967 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000335972892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335972892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000335972892 none C[C@H]1C(=O)NCCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6] 27 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]) total number of confs: 41 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335972892 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 Building ZINC000335972892 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000335972892 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 966) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000335972892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000335972892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000335972892 none C[C@H]1C(=O)NCCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6] 26 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 967) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)NCCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000335972892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000335972892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000335972892 none C[C@H]1C(=O)NCCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6] 27 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]) total number of confs: 41 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000335972892 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000335972892 Building ZINC000336153985 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336153985 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/968 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000336153985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336153985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153985 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 7, 7, 10, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/969 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000336153985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336153985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153985 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 10, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336153985 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 Building ZINC000336153985 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336153985 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 968) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000336153985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336153985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153985 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 7, 7, 10, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 969) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O) `ZINC000336153985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336153985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153985 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 10, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336153985 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153985 Building ZINC000336153986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336153986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/970 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000336153986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336153986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153986 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 7, 7, 18, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 7, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/971 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000336153986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336153986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153986 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 7, 7, 16, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336153986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 Building ZINC000336153986 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336153986 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 970) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000336153986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336153986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153986 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 7, 7, 18, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 7, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 971) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O) `ZINC000336153986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336153986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336153986 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 11, 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, 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] 0 hydrogens need 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, 1, 1, 1, 1, 7, 7, 16, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336153986 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336153986 Building ZINC000336381817 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336381817 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/972 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000336381817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336381817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381817 none CC[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8] 44 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/973 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000336381817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336381817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381817 none CC[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 40 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336381817 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 Building ZINC000336381817 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336381817 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 972) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000336381817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336381817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381817 none CC[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8] 44 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 973) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000336381817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336381817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381817 none CC[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 40 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336381817 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381817 Building ZINC000336381818 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336381818 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/974 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000336381818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336381818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381818 none CC[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7] 34 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/975 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000336381818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336381818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381818 none CC[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8] 33 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336381818 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 Building ZINC000336381818 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336381818 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 974) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000336381818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336381818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381818 none CC[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7] 34 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 975) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000336381818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336381818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC000336381818 none CC[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 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, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 14, 14, 14, 14, 9, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8] 33 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336381818 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336381818 Building ZINC000336479847 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336479847 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/976 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1=O) `ZINC000336479847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336479847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336479847 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 34, 34, 34, 34, 34, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/977 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1=O) `ZINC000336479847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336479847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336479847 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 32, 32, 32, 32, 32, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336479847 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 Building ZINC000336479847 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336479847 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 976) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1=O) `ZINC000336479847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336479847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336479847 none CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 34, 34, 34, 34, 34, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 977) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1=O) `ZINC000336479847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336479847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336479847 none CCN1CCN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 18, 18, 18, 10, 2, 15, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 32, 32, 32, 32, 32, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336479847 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336479847 Building ZINC000336516303 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336516303 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/978 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C) `ZINC000336516303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336516303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336516303 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 11, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 23 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 30 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/979 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C) `ZINC000336516303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336516303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336516303 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 11, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 22 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 30 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336516303 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 Building ZINC000336516303 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336516303 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 978) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C) `ZINC000336516303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336516303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336516303 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 11, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 23 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 30 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 979) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C) `ZINC000336516303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336516303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000336516303 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 11, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 22 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 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: 30 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000336516303 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000336516303 Building ZINC000337048333 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337048333 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/980 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)cc1) `ZINC000337048333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337048333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000337048333 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 5, 1, 8, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 35, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 35, 35, 50, 50, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/981 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)cc1) `ZINC000337048333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337048333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000337048333 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 5, 1, 8, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 36, 50, 50, 9, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 36, 36, 50, 50, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337048333 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 Building ZINC000337048333 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337048333 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 980) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)cc1) `ZINC000337048333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337048333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000337048333 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 5, 1, 8, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 35, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 35, 35, 50, 50, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 981) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)cc1) `ZINC000337048333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337048333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000337048333 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(CC(N)=O)n2)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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 5, 1, 8, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 36, 50, 50, 9, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 36, 36, 50, 50, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337048333 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337048333 Building ZINC000337058648 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337058648 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/982 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1) `ZINC000337058648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337058648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058648 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 19, 25, 6, 6, 16, 16, 16, 16, 16, 6, 2, 3, 3, 3, 8, 19, 19, 25, 25, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/983 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1) `ZINC000337058648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337058648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058648 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 16, 23, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 7, 16, 16, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337058648 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 Building ZINC000337058648 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337058648 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 982) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1) `ZINC000337058648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337058648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058648 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 19, 25, 6, 6, 16, 16, 16, 16, 16, 6, 2, 3, 3, 3, 8, 19, 19, 25, 25, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 983) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1) `ZINC000337058648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337058648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058648 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 16, 23, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 7, 16, 16, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337058648 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058648 Building ZINC000337058649 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337058649 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/984 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1) `ZINC000337058649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337058649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058649 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 16, 23, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 7, 16, 16, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/985 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1) `ZINC000337058649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337058649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058649 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 18, 24, 5, 5, 15, 15, 15, 15, 15, 5, 2, 3, 3, 3, 8, 18, 18, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337058649 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 Building ZINC000337058649 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337058649 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 984) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1) `ZINC000337058649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337058649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058649 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 16, 23, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 7, 16, 16, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 985) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1) `ZINC000337058649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337058649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000337058649 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 18, 24, 5, 5, 15, 15, 15, 15, 15, 5, 2, 3, 3, 3, 8, 18, 18, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337058649 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337058649 Building ZINC000337069369 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337069369 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/986 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/986' -> `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@H](C)C(=O)NCCF) `ZINC000337069369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337069369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069369 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 24, 24, 24, 45, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 24, 45, 45, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/987 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/987' -> `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@H](C)C(=O)NCCF) `ZINC000337069369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337069369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069369 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 19, 19, 19, 38, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 19, 38, 38, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337069369 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 Building ZINC000337069369 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337069369 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 986) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF) `ZINC000337069369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337069369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069369 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 24, 24, 24, 45, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 24, 45, 45, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 987) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF) `ZINC000337069369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337069369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069369 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 19, 19, 19, 38, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 19, 38, 38, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 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: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337069369 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069369 Building ZINC000337069381 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337069381 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/988 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/988' -> `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@@H](C)C(=O)NCCF) `ZINC000337069381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337069381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069381 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 19, 19, 19, 37, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 19, 37, 37, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/989 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/989' -> `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@@H](C)C(=O)NCCF) `ZINC000337069381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337069381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069381 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 25, 25, 25, 45, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 12, 12, 12, 25, 45, 45, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337069381 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 Building ZINC000337069381 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337069381 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 988) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF) `ZINC000337069381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337069381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069381 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 19, 19, 19, 37, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 19, 37, 37, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 989) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF) `ZINC000337069381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337069381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000337069381 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)NCCF 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', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 15, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 25, 25, 25, 45, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 12, 12, 12, 25, 45, 45, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337069381 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337069381 Building ZINC000337108850 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337108850 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/990 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337108850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108850 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [13, 5, 13, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 13, 27, 27, 31, 31, 31, 31, 13, 13, 13, 5, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/991 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337108850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108850 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 15, 26, 26, 28, 28, 28, 28, 15, 15, 15, 5, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337108850 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 Building ZINC000337108850 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337108850 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 990) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337108850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108850 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [13, 5, 13, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 13, 27, 27, 31, 31, 31, 31, 13, 13, 13, 5, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 991) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337108850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108850 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 15, 26, 26, 28, 28, 28, 28, 15, 15, 15, 5, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337108850 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108850 Building ZINC000337108851 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337108851 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/992 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337108851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108851 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [13, 4, 13, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 23, 23, 24, 24, 24, 24, 13, 13, 13, 4, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/993 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337108851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108851 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 26, 26, 28, 28, 28, 28, 12, 12, 12, 4, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337108851 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 Building ZINC000337108851 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337108851 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 992) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337108851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108851 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [13, 4, 13, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 23, 23, 24, 24, 24, 24, 13, 13, 13, 4, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 993) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1) `ZINC000337108851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337108851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337108851 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 26, 26, 28, 28, 28, 28, 12, 12, 12, 4, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337108851 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337108851 Building ZINC000337143537 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337143537 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/994 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337143537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143537 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 23, 4, 9, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 9, 23, 23, 24, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10, 10, 10, 23, 23] 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]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/995 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337143537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143537 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 4, 10, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337143537 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 Building ZINC000337143537 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337143537 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 994) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337143537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143537 none CC(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 23, 4, 9, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 9, 23, 23, 24, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10, 10, 10, 23, 23] 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]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 995) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337143537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143537 none CC(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 4, 10, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337143537 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143537 Building ZINC000337143538 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337143538 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/996 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337143538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143538 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 25, 4, 10, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/997 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337143538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143538 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 24, 4, 9, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 9, 23, 23, 24, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10, 10, 10, 23, 23] 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]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337143538 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 Building ZINC000337143538 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337143538 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 996) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337143538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143538 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 25, 4, 10, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 997) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC000337143538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337143538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000337143538 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 24, 4, 9, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 9, 23, 23, 24, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10, 10, 10, 23, 23] 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]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337143538 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337143538 Building ZINC000337191274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337191274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/998 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC000337191274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337191274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337191274 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 28, 28, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 11, 11, 2, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/999 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC000337191274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337191274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337191274 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 28, 28, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 11, 11, 2, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337191274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 Building ZINC000337191274 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337191274 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 998) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC000337191274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337191274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337191274 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 28, 28, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 11, 11, 2, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 mkdir: created directory `1' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 1 (index: 999) grep: /scratch/xiaobo/121205/xcw-8058088.75/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC000337191274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337191274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000337191274 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 28, 28, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 11, 11, 2, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337191274 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/0.* 1: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274/1.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337191274 Building ZINC000337386755 mkdir: created directory `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000337386755 mkdir: created directory `0' /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755/0 /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/121205/xcw-8058088.75/working/3D/1000 `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000337386755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337386755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000337386755 none CN(C)C[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 18, 25, 25, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 75, 18, 18, 5, 11, 11, 11, 11, 11] 150 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]) total number of confs: 187 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755 /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Finished preparing ZINC000337386755 Recording results /scratch/xiaobo/121205/xcw-8058088.75/working /scratch/xiaobo/121205/xcw-8058088.75 Appending to /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.* 0: /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755/0.* Removing working files in /scratch/xiaobo/121205/xcw-8058088.75/working/building/ZINC000337386755 /scratch/xiaobo/121205/xcw-8058088.75 Compressing combined databse files /scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/121205/xcw-8058088.75/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/121205/xcw-8058088.75/working/3D/1001' removed directory: `/scratch/xiaobo/121205/xcw-8058088.75/working/3D' rmdir: removing directory, `/scratch/xiaobo/121205/xcw-8058088.75/working/building' rmdir: removing directory, `/scratch/xiaobo/121205/xcw-8058088.75/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/121205/xcw-8058088.75' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xcw' `/scratch/xiaobo/121205/xcw-8058088.75/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xcw/finished' `/scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xcw/finished/xcw.db2.gz' removed `/scratch/xiaobo/121205/xcw-8058088.75/finished/xcw.db2.gz' removed directory: `/scratch/xiaobo/121205/xcw-8058088.75/finished' removed directory: `/scratch/xiaobo/121205/xcw-8058088.75'